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 6 28-FEB-24 5K7N 1 REMARK 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