HEADER PROTEIN FIBRIL 26-MAY-16 5K7N TITLE MICROED STRUCTURE OF TAU VQIVYK PEPTIDE AT 1.1 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VQIVYK; COMPND 3 CHAIN: Z; COMPND 4 SYNONYM: TAU PEPTIDE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR M.J.DE LA CRUZ,J.HATTNE,D.SHI,P.SEIDLER,J.RODRIGUEZ,F.E.REYES, AUTHOR 2 M.R.SAWAYA,D.CASCIO,D.EISENBERG,T.GONEN REVDAT 5 18-DEC-19 5K7N 1 REMARK REVDAT 4 22-AUG-18 5K7N 1 REMARK REVDAT 3 13-SEP-17 5K7N 1 REMARK REVDAT 2 12-APR-17 5K7N 1 JRNL REVDAT 1 05-APR-17 5K7N 0 JRNL AUTH M.J.DE LA CRUZ,J.HATTNE,D.SHI,P.SEIDLER,J.RODRIGUEZ, JRNL AUTH 2 F.E.REYES,M.R.SAWAYA,D.CASCIO,S.C.WEISS,S.K.KIM,C.S.HINCK, JRNL AUTH 3 A.P.HINCK,G.CALERO,D.EISENBERG,T.GONEN JRNL TITL ATOMIC-RESOLUTION STRUCTURES FROM FRAGMENTED PROTEIN JRNL TITL 2 CRYSTALS WITH THE CRYOEM METHOD MICROED. JRNL REF NAT. METHODS V. 14 399 2017 JRNL REFN ESSN 1548-7105 JRNL PMID 28192420 JRNL DOI 10.1038/NMETH.4178 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.1 REMARK 3 NUMBER OF REFLECTIONS : 1898 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 190 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.11 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 543 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2117 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 489 REMARK 3 BIN R VALUE (WORKING SET) : 0.2104 REMARK 3 BIN FREE R VALUE : 0.2243 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.94 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 54 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 53 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.66020 REMARK 3 B22 (A**2) : 0.06780 REMARK 3 B33 (A**2) : -1.72800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.18980 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.203 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.046 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.046 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.048 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.045 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 111 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 202 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 26 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 2 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 12 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 111 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 7 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 68 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 0.77 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.62 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 9.65 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { Z|* } REMARK 3 ORIGIN FOR THE GROUP (A): 10.8417 1.9560 8.5763 REMARK 3 T TENSOR REMARK 3 T11: -0.0041 T22: -0.0667 REMARK 3 T33: 0.0721 T12: -0.0004 REMARK 3 T13: 0.0615 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.4341 L22: 0.6654 REMARK 3 L33: 0.0381 L12: 0.2835 REMARK 3 L13: 0.1240 L23: 0.2447 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: 0.0028 S13: 0.0020 REMARK 3 S21: -0.0426 S22: 0.0046 S23: 0.0052 REMARK 3 S31: 0.0280 S32: 0.0029 S33: 0.0092 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5K7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221815. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 3319 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 240 RESOLUTION RANGE LOW (A) : 14.700 REMARK 240 DATA SCALING SOFTWARE : NULL REMARK 240 COMPLETENESS FOR RANGE (%) : 83.0 REMARK 240 DATA REDUNDANCY : 1.900 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.10 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.23 REMARK 240 COMPLETENESS FOR SHELL (%) : 79.4 REMARK 240 DATA REDUNDANCY IN SHELL : 1.80 REMARK 240 R MERGE FOR SHELL (I) : 0.47200 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 14.71000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.71000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.49500 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 300 REMARK: THE BIOLOGICAL UNIT IS AN EXTENDED PAIR OF BETA SHEETS REMARK 300 COMPRISING PEPTIDES AT POSITION X,Y,Z EXTENDED AD INFINITUM ALONG REMARK 300 THE B CRYSTAL AXIS. 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: NONAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z 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 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -19.96000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -14.97000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -9.98000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -4.99000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 4.99000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 9.98000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 14.97000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 19.96000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-8216 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8217 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8218 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8219 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8220 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8221 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8222 RELATED DB: EMDB REMARK 900 RELATED ID: 5K7O RELATED DB: PDB REMARK 900 RELATED ID: 5K7P RELATED DB: PDB REMARK 900 RELATED ID: 5K7Q RELATED DB: PDB REMARK 900 RELATED ID: 5K7R RELATED DB: PDB REMARK 900 RELATED ID: 5K7S RELATED DB: PDB REMARK 900 RELATED ID: 5K7T RELATED DB: PDB DBREF 5K7N Z 1 6 PDB 5K7N 5K7N 1 6 SEQRES 1 Z 6 VAL GLN ILE VAL TYR LYS FORMUL 2 HOH *2(H2 O) CRYST1 29.420 4.990 37.170 90.00 111.55 90.00 C 1 2 1 4 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 0.033990 0.000000 0.013423 0.00000 SCALE2 0.000000 0.200401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028925 0.00000 MASTER 249 0 0 0 0 0 0 6 0 0 0 1 END