1N7A - Header Asymmetric Unit

HEADER DNA, RNA 13-NOV-02 1N7A

TITLE RIP-RADIATION-DAMAGE INDUCED PHASING

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3'); COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE RNA HEXAMER UGAGGU WHERE THE 2ND G WAS COMPND 6 REPLACED BY A C8-BROMINATED GD WAS PHASED USING RADIATION COMPND 7 DAMAGE ON THE HIGHLY SUSCEPTIBLE BR-C8 BOND.

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE DNA/RNA HYBRID WAS SYNTHESIZED BY THE SOURCE 4 PHOSPHORAMIDITE METHOD USING AN APPLIED BIOSYSTEM DNA SOURCE 5 SYNTHESIZER 391

KEYWDS DNA, RNA

EXPDTA X-RAY DIFFRACTION

AUTHOR R.B.G.RAVELLI,H.-K.S.LEIROS,B.PAN,M.CAFFREY,S.MCSWEENEY

REVDAT 3 24-FEB-09 1N7A 1 VERSN REVDAT 2 13-JUN-06 1N7A 1 ATOM JRNL REVDAT 1 04-MAR-03 1N7A 0

JRNL AUTH R.B.G.RAVELLI,H.-K.S.LEIROS,B.PAN,M.CAFFREY, JRNL AUTH 2 S.MCSWEENEY JRNL TITL SPECIFIC RADIATION-DAMAGE CAN BE USED TO SOLVE JRNL TITL 2 MACROMOLECULAR CRYSTAL STRUCTURES JRNL REF STRUCTURE V. 11 217 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12575941 JRNL DOI 10.1016/S0969-2126(03)00006-6

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 35974 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1802 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4872 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE SET COUNT : 268 REMARK 3 BIN FREE R VALUE : 0.2080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1024 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 181 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.034 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.036 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.459 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1171 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1778 ; 1.533 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 184 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 520 ; 0.019 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 447 ; 0.374 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 153 ; 0.081 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 44 ; 0.133 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.144 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1164 ; 2.120 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1778 ; 2.790 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1144 ; 1.164 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 17 ; 2.853 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1016 ; 4.684 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1N7A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-02. REMARK 100 THE RCSB ID CODE IS RCSB017607.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : DIAMOND(111) AND GE(200) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PRODC REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35974 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.240 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.19 REMARK 200 R MERGE FOR SHELL (I) : 0.34100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELXD, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MM (SINGLE STRAND) RNA, 20 MM REMARK 280 SODIUM CACODYLATE BUFFER, PH 6.0, 5 MM SPERMINE TETRACHLORIDE, REMARK 280 32 MM KCL AND 2 % (V/V) METHYL-2,4-PENTANEDIOL (MPD) AGAINST REMARK 280 25 % MPD IN THE RESERVOIR, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 15.61650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.32550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.55100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.32550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.61650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.55100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.

REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SPM H 501

REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U C 6 O4 REMARK 620 2 U H 6 O4 75.7 REMARK 620 3 G H 5 O6 99.5 68.1 REMARK 620 4 U A 6 O4 75.9 120.6 167.7 REMARK 620 5 U D 6 O4 121.2 76.1 115.6 76.1 REMARK 620 6 G A 5 O6 113.7 169.6 104.9 67.6 101.3 REMARK 620 7 G C 5 O6 66.3 114.0 67.7 100.1 169.5 68.3 REMARK 620 8 G D 5 O6 168.2 101.6 69.0 114.7 68.3 68.3 105.4 REMARK 620 9 K A 104 K 117.3 120.3 52.6 119.0 121.4 52.3 51.6 53.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 104 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G H 4 O6 REMARK 620 2 G H 5 O6 72.0 REMARK 620 3 G A 4 O6 116.9 158.8 REMARK 620 4 G A 5 O6 160.6 106.8 71.3 REMARK 620 5 G C 4 O6 73.5 126.7 74.3 93.4 REMARK 620 6 G C 5 O6 91.4 69.8 126.3 70.6 71.7 REMARK 620 7 G D 4 O6 73.6 91.8 73.9 125.6 115.6 159.5 REMARK 620 8 G D 5 O6 126.0 69.2 91.1 68.7 160.1 108.4 71.6 REMARK 620 9 K A 109 K 57.9 126.1 59.0 127.1 58.0 125.9 57.6 125.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 105 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BGM D 2 O6 REMARK 620 2 BGM F 2 O6 86.3 REMARK 620 3 BGM A 2 O6 68.0 146.1 REMARK 620 4 BGM C 2 O6 105.5 143.4 67.9 REMARK 620 5 BGM H 2 O6 69.0 84.7 104.8 68.4 REMARK 620 6 K A 108 K 53.0 127.2 52.4 52.5 52.4 REMARK 620 7 BGM B 2 O6 141.0 104.9 84.5 87.7 147.8 127.9 REMARK 620 8 BGM E 2 O6 82.9 67.3 87.3 147.3 141.6 127.1 68.2 REMARK 620 9 BGM G 2 O6 147.2 68.6 142.8 85.2 87.3 128.0 68.7 104.9 REMARK 620 10 K E 106 K 126.1 51.8 128.1 128.4 127.0 178.9 53.1 REMARK 620 52.6 52.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 9 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 108 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BGM D 2 O6 REMARK 620 2 A D 3 N1 62.2 REMARK 620 3 A H 3 N1 109.2 79.6 REMARK 620 4 BGM A 2 O6 66.7 109.1 165.1 REMARK 620 5 A A 3 N1 99.1 80.5 131.8 62.7 REMARK 620 6 BGM C 2 O6 102.2 163.3 101.7 66.4 109.4 REMARK 620 7 A C 3 N1 164.6 132.5 81.0 100.4 81.1 63.6 REMARK 620 8 BGM H 2 O6 67.8 99.7 63.0 102.9 164.3 67.0 109.1 REMARK 620 9 K A 109 K 127.7 65.9 66.1 128.3 65.8 130.1 66.6 128.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 109 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 3 N1 REMARK 620 2 A A 3 N1 80.6 REMARK 620 3 G D 4 O6 125.3 69.2 REMARK 620 4 G C 4 O6 86.3 151.9 99.5 REMARK 620 5 G A 4 O6 69.0 86.8 64.9 65.2 REMARK 620 6 A H 3 N1 80.5 132.6 151.8 68.3 125.1 REMARK 620 7 A D 3 N1 131.7 81.0 87.9 125.4 152.8 80.1 REMARK 620 8 G H 4 O6 151.5 125.8 65.4 65.3 99.2 86.5 69.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 K B 102 K REMARK 620 2 G B 5 O6 53.6 REMARK 620 3 U B 6 O4 119.9 67.0 REMARK 620 4 G E 5 O6 53.6 69.1 99.4 REMARK 620 5 U E 6 O4 119.8 115.3 76.0 67.0 REMARK 620 6 G G 5 O6 52.1 68.7 115.6 105.7 167.7 REMARK 620 7 U G 6 O4 119.4 99.8 76.2 168.8 120.8 67.9 REMARK 620 8 G F 5 O6 52.0 105.6 167.8 68.6 99.8 68.0 115.3 REMARK 620 9 U F 6 O4 118.1 168.1 122.0 114.1 75.7 99.6 76.6 66.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G E 4 O6 REMARK 620 2 G B 4 O6 74.2 REMARK 620 3 G F 4 O6 73.3 115.8 REMARK 620 4 G G 4 O6 115.5 73.4 73.2 REMARK 620 5 K B 107 K 57.7 58.0 57.8 57.8 REMARK 620 6 G B 5 O6 91.8 73.1 158.5 128.0 126.9 REMARK 620 7 G E 5 O6 72.6 127.4 92.0 159.0 126.6 68.4 REMARK 620 8 G F 5 O6 126.3 158.8 71.2 90.9 125.1 108.0 69.9 REMARK 620 9 G G 5 O6 158.9 90.6 127.4 72.4 126.1 69.4 107.3 70.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 107 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G E 4 O6 REMARK 620 2 A F 3 N1 68.7 REMARK 620 3 A E 3 N1 86.0 80.7 REMARK 620 4 K E 106 K 128.3 65.3 64.7 REMARK 620 5 G B 4 O6 65.4 126.0 69.3 129.6 REMARK 620 6 G F 4 O6 64.9 86.0 150.8 131.5 98.8 REMARK 620 7 G G 4 O6 99.1 150.9 126.1 132.6 64.9 65.0 REMARK 620 8 A B 3 N1 152.1 132.6 81.4 67.3 86.8 125.8 69.5 REMARK 620 9 A G 3 N1 125.5 80.2 132.5 67.8 151.5 69.4 86.8 80.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K E 106 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BGM G 2 O6 REMARK 620 2 A E 3 N1 164.3 REMARK 620 3 BGM E 2 O6 102.2 63.6 REMARK 620 4 BGM F 2 O6 67.6 109.5 66.3 REMARK 620 5 A F 3 N1 108.6 82.2 102.2 63.7 REMARK 620 6 A G 3 N1 62.4 132.3 163.7 101.0 79.6 REMARK 620 7 BGM B 2 O6 66.8 99.8 66.4 102.2 165.3 108.7 REMARK 620 8 A B 3 N1 98.3 81.6 110.5 163.4 131.7 78.6 62.9 REMARK 620 N 1 2 3 4 5 6 7

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 101 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 102 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 103 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 104 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 105 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K E 106 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 107 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 108 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 109 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM H 501 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM B 502

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N7B RELATED DB: PDB REMARK 900 RNA/DNA MODEL REFINED AGAINST DATA COLLECTED AFTER "X-RAY REMARK 900 BURN" REMARK 900 RELATED ID: 1N6X RELATED DB: PDB REMARK 900 TRYPSIN MODEL REFINED AGAINST DATA COLLECTED BEFORE "X-RAY REMARK 900 BURN" REMARK 900 RELATED ID: 1N6Y RELATED DB: PDB REMARK 900 TRYPSIN MODEL REFINED AGAINST DATA COLLECTED AFTER "X-RAY REMARK 900 BURN"

DBREF 1N7A A 1 6 PDB 1N7A 1N7A 1 6 DBREF 1N7A B 1 6 PDB 1N7A 1N7A 1 6 DBREF 1N7A C 1 6 PDB 1N7A 1N7A 1 6 DBREF 1N7A D 1 6 PDB 1N7A 1N7A 1 6 DBREF 1N7A E 1 6 PDB 1N7A 1N7A 1 6 DBREF 1N7A F 1 6 PDB 1N7A 1N7A 1 6 DBREF 1N7A G 1 6 PDB 1N7A 1N7A 1 6 DBREF 1N7A H 1 6 PDB 1N7A 1N7A 1 6

SEQRES 1 A 6 U BGM A G G U SEQRES 1 B 6 U BGM A G G U SEQRES 1 C 6 U BGM A G G U SEQRES 1 D 6 U BGM A G G U SEQRES 1 E 6 U BGM A G G U SEQRES 1 F 6 U BGM A G G U SEQRES 1 G 6 U BGM A G G U SEQRES 1 H 6 U BGM A G G U

MODRES 1N7A BGM A 2 DG MODRES 1N7A BGM B 2 DG MODRES 1N7A BGM C 2 DG MODRES 1N7A BGM D 2 DG MODRES 1N7A BGM E 2 DG MODRES 1N7A BGM F 2 DG MODRES 1N7A BGM G 2 DG MODRES 1N7A BGM H 2 DG

HET BGM A 2 23 HET BGM B 2 23 HET BGM C 2 23 HET BGM D 2 23 HET BGM E 2 23 HET BGM F 2 23 HET BGM G 2 23 HET BGM H 2 23 HET K B 101 1 HET K B 102 1 HET K A 103 1 HET K A 104 1 HET K A 105 1 HET K E 106 1 HET K B 107 1 HET K A 108 1 HET K A 109 1 HET SPM H 501 8 HET SPM B 502 14

HETNAM BGM 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETNAM K POTASSIUM ION HETNAM SPM SPERMINE

FORMUL 1 BGM 8(C10 H13 BR N5 O7 P) FORMUL 9 K 9(K 1+) FORMUL 18 SPM 2(C10 H26 N4) FORMUL 20 HOH *181(H2 O)

LINK O3' U A 1 P BGM A 2 1555 1555 1.58 LINK O3' BGM A 2 P A A 3 1555 1555 1.61 LINK K K A 103 O4 U C 6 1555 1555 2.73 LINK K K A 103 O4 U H 6 1555 1555 2.71 LINK K K A 103 O6 G H 5 1555 1555 2.86 LINK K K A 103 O4 U A 6 1555 1555 2.77 LINK K K A 103 O4 U D 6 1555 1555 2.67 LINK K K A 103 O6 G A 5 1555 1555 2.86 LINK K K A 103 O6 G C 5 1555 1555 2.93 LINK K K A 103 O6 G D 5 1555 1555 2.88 LINK K K A 103 K K A 104 1555 1555 3.43 LINK K K A 104 O6 G H 4 1555 1555 2.76 LINK K K A 104 O6 G H 5 1555 1555 2.84 LINK K K A 104 O6 G A 4 1555 1555 2.76 LINK K K A 104 O6 G A 5 1555 1555 2.82 LINK K K A 104 O6 G C 4 1555 1555 2.77 LINK K K A 104 O6 G C 5 1555 1555 2.81 LINK K K A 104 O6 G D 4 1555 1555 2.75 LINK K K A 104 O6 G D 5 1555 1555 2.90 LINK K K A 104 K K A 109 1555 1555 3.45 LINK K K A 105 O6 BGM D 2 1555 1555 2.89 LINK K K A 105 O6 BGM F 2 1555 1555 2.87 LINK K K A 105 O6 BGM A 2 1555 1555 2.87 LINK K K A 105 O6 BGM C 2 1555 1555 2.84 LINK K K A 105 O6 BGM H 2 1555 1555 2.88 LINK K K A 105 K K A 108 1555 1555 3.57 LINK K K A 105 O6 BGM B 2 1555 1555 2.87 LINK K K A 105 O6 BGM E 2 1555 1555 2.88 LINK K K A 105 O6 BGM G 2 1555 1555 2.86 LINK K K A 105 K K E 106 1555 1555 3.59 LINK K K A 108 O6 BGM D 2 1555 1555 2.94 LINK K K A 108 N1 A D 3 1555 1555 3.48 LINK K K A 108 N1 A H 3 1555 1555 3.45 LINK K K A 108 O6 BGM A 2 1555 1555 2.91 LINK K K A 108 N1 A A 3 1555 1555 3.43 LINK K K A 108 O6 BGM C 2 1555 1555 2.91 LINK K K A 108 N1 A C 3 1555 1555 3.37 LINK K K A 108 O6 BGM H 2 1555 1555 2.91 LINK K K A 108 K K A 109 1555 1555 2.78 LINK K K A 109 N1 A C 3 1555 1555 3.41 LINK K K A 109 N1 A A 3 1555 1555 3.41 LINK K K A 109 O6 G D 4 1555 1555 3.05 LINK K K A 109 O6 G C 4 1555 1555 3.07 LINK K K A 109 O6 G A 4 1555 1555 3.12 LINK K K A 109 N1 A H 3 1555 1555 3.44 LINK K K A 109 N1 A D 3 1555 1555 3.45 LINK K K A 109 O6 G H 4 1555 1555 3.06 LINK O3' U B 1 P BGM B 2 1555 1555 1.60 LINK O3' BGM B 2 P A B 3 1555 1555 1.59 LINK K K B 101 K K B 102 1555 1555 3.41 LINK K K B 101 O6 G B 5 1555 1555 2.83 LINK K K B 101 O4 U B 6 1555 1555 2.72 LINK K K B 101 O6 G E 5 1555 1555 2.84 LINK K K B 101 O4 U E 6 1555 1555 2.77 LINK K K B 101 O6 G G 5 1555 1555 2.89 LINK K K B 101 O4 U G 6 1555 1555 2.75 LINK K K B 101 O6 G F 5 1555 1555 2.93 LINK K K B 101 O4 U F 6 1555 1555 2.70 LINK K K B 102 O6 G E 4 1555 1555 2.76 LINK K K B 102 O6 G B 4 1555 1555 2.76 LINK K K B 102 O6 G F 4 1555 1555 2.77 LINK K K B 102 O6 G G 4 1555 1555 2.78 LINK K K B 102 K K B 107 1555 1555 3.48 LINK K K B 102 O6 G B 5 1555 1555 2.86 LINK K K B 102 O6 G E 5 1555 1555 2.86 LINK K K B 102 O6 G F 5 1555 1555 2.81 LINK K K B 102 O6 G G 5 1555 1555 2.81 LINK K K B 107 O6 G E 4 1555 1555 3.08 LINK K K B 107 N1 A F 3 1555 1555 3.41 LINK K K B 107 N1 A E 3 1555 1555 3.45 LINK K K B 107 K K E 106 1555 1555 2.77 LINK K K B 107 O6 G B 4 1555 1555 3.09 LINK K K B 107 O6 G F 4 1555 1555 3.08 LINK K K B 107 O6 G G 4 1555 1555 3.09 LINK K K B 107 N1 A B 3 1555 1555 3.41 LINK K K B 107 N1 A G 3 1555 1555 3.41 LINK O3' U C 1 P BGM C 2 1555 1555 1.59 LINK O3' BGM C 2 P A C 3 1555 1555 1.59 LINK O3' U D 1 P BGM D 2 1555 1555 1.60 LINK O3' BGM D 2 P A D 3 1555 1555 1.59 LINK O3' U E 1 P BGM E 2 1555 1555 1.59 LINK O3' BGM E 2 P A E 3 1555 1555 1.60 LINK K K E 106 O6 BGM G 2 1555 1555 2.92 LINK K K E 106 N1 A E 3 1555 1555 3.38 LINK K K E 106 O6 BGM E 2 1555 1555 2.93 LINK K K E 106 O6 BGM F 2 1555 1555 2.89 LINK K K E 106 N1 A F 3 1555 1555 3.38 LINK K K E 106 N1 A G 3 1555 1555 3.49 LINK K K E 106 O6 BGM B 2 1555 1555 2.96 LINK K K E 106 N1 A B 3 1555 1555 3.47 LINK O3' U F 1 P BGM F 2 1555 1555 1.60 LINK O3' BGM F 2 P A F 3 1555 1555 1.61 LINK O3' U G 1 P BGM G 2 1555 1555 1.59 LINK O3' BGM G 2 P A G 3 1555 1555 1.62 LINK O3' U H 1 P BGM H 2 1555 1555 1.59 LINK O3' BGM H 2 P A H 3 1555 1555 1.61

SITE 1 AC1 9 G B 5 U B 6 K B 102 G E 5 SITE 2 AC1 9 U E 6 G F 5 U F 6 G G 5 SITE 3 AC1 9 U G 6 SITE 1 AC2 10 G B 4 G B 5 K B 101 K B 107 SITE 2 AC2 10 G E 4 G E 5 G F 4 G F 5 SITE 3 AC2 10 G G 4 G G 5 SITE 1 AC3 9 G A 5 U A 6 K A 104 G C 5 SITE 2 AC3 9 U C 6 G D 5 U D 6 G H 5 SITE 3 AC3 9 U H 6 SITE 1 AC4 10 G A 4 G A 5 K A 103 K A 109 SITE 2 AC4 10 G C 4 G C 5 G D 4 G D 5 SITE 3 AC4 10 G H 4 G H 5 SITE 1 AC5 10 BGM A 2 K A 108 BGM B 2 BGM C 2 SITE 2 AC5 10 BGM D 2 BGM E 2 K E 106 BGM F 2 SITE 3 AC5 10 BGM G 2 BGM H 2 SITE 1 AC6 10 K A 105 BGM B 2 A B 3 K B 107 SITE 2 AC6 10 BGM E 2 A E 3 BGM F 2 A F 3 SITE 3 AC6 10 BGM G 2 A G 3 SITE 1 AC7 10 A B 3 G B 4 K B 102 A E 3 SITE 2 AC7 10 G E 4 K E 106 A F 3 G F 4 SITE 3 AC7 10 A G 3 G G 4 SITE 1 AC8 10 BGM A 2 A A 3 K A 105 K A 109 SITE 2 AC8 10 BGM C 2 A C 3 BGM D 2 A D 3 SITE 3 AC8 10 BGM H 2 A H 3 SITE 1 AC9 10 A A 3 G A 4 K A 104 K A 108 SITE 2 AC9 10 A C 3 G C 4 A D 3 G D 4 SITE 3 AC9 10 A H 3 G H 4 SITE 1 BC1 6 A D 3 G D 4 A F 3 BGM H 2 SITE 2 BC1 6 HOH H 234 HOH H 331 SITE 1 BC2 12 BGM A 2 A A 3 BGM B 2 A B 3 SITE 2 BC2 12 HOH B 269 HOH C 263 HOH C 309 BGM D 2 SITE 3 BC2 12 A D 3 HOH D 341 BGM E 2 A E 3

CRYST1 31.233 51.102 70.651 90.00 90.00 90.00 P 21 21 21 32

ORIGX1 1.000000 0.000000 0.000000 0.00000

ORIGX2 0.000000 1.000000 0.000000 0.00000

ORIGX3 0.000000 0.000000 1.000000 0.00000

SCALE1 0.032017 0.000000 0.000000 0.00000

SCALE2 0.000000 0.019569 0.000000 0.00000

SCALE3 0.000000 0.000000 0.014154 0.00000