HEADER PROTEIN FIBRIL 15-OCT-24 9DYW TITLE RACEMIC MIXTURE OF PEPTIDE VVGGVV FORMS RIPPLED SHEETS COMPND MOL_ID: 1; COMPND 2 MOLECULE: VVGGVV; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RIPPLED SHEET, RACEMIC MIXTURE, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SAWAYA,J.A.RASKATOV,A.HAZARI REVDAT 2 16-APR-25 9DYW 1 JRNL REVDAT 1 26-MAR-25 9DYW 0 JRNL AUTH A.HAZARI,M.R.SAWAYA,H.LEE,M.SAJIMON,H.KIM,W.A.GODDARD III, JRNL AUTH 2 D.EISENBERG,J.A.RASKATOV JRNL TITL FORMATION OF RIPPLED BETA-SHEETS FROM MIXED CHIRALITY LINEAR JRNL TITL 2 AND CYCLIC PEPTIDES-NEW STRUCTURAL MOTIFS BASED ON THE JRNL TITL 3 PAULING-COREY RIPPLED BETA-SHEET. JRNL REF CHEM SCI V. 16 5907 2025 JRNL REFN ISSN 2041-6520 JRNL PMID 40060095 JRNL DOI 10.1039/D4SC08079C REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 4615 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.011 REMARK 3 FREE R VALUE TEST SET COUNT : 462 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1002 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.1740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 74 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00600 REMARK 3 B22 (A**2) : 0.52400 REMARK 3 B33 (A**2) : -0.53300 REMARK 3 B12 (A**2) : -0.11100 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : 0.15700 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.029 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.029 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.014 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.632 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 77 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 96 ; 0.007 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 107 ; 1.958 ; 1.611 REMARK 3 BOND ANGLES OTHERS (DEGREES): 215 ; 1.364 ; 1.628 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 12 ; 7.268 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 9 ; 8.558 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 9 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 93 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 11 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 12 ; 0.072 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 29 ; 0.096 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 43 ; 0.134 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 7 ; 0.062 ; 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 48 ; 0.492 ; 0.588 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 47 ; 0.497 ; 0.586 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 57 ; 0.654 ; 0.891 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 58 ; 0.648 ; 0.892 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 29 ; 0.618 ; 0.689 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 29 ; 0.615 ; 0.693 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 49 ; 0.806 ; 1.009 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 49 ; 0.806 ; 1.011 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 173 ; 1.336 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9DYW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1000289062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979330 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20230630 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20230630 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4615 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXD 2013/2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NEEDLE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% HEXAFLUOROISOPROPANOL IN WATER, PH REMARK 280 3, BATCH MODE, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P -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 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 3.73347 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -15.03334 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 -3.73347 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 15.03334 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 7.46693 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -30.06668 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 3.73347 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -15.03334 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 -3.73347 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 15.03334 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 7.46693 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -30.06668 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 DBREF 9DYW A 1 6 PDB 9DYW 9DYW 1 6 DBREF 9DYW B 1 6 PDB 9DYW 9DYW 1 6 SEQRES 1 A 6 VAL VAL GLY GLY VAL VAL SEQRES 1 B 6 VAL VAL GLY GLY VAL VAL FORMUL 3 HOH *10(H2 O) CRYST1 22.950 15.490 9.520 88.67 92.76 103.95 P -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 0.043573 0.010821 0.001973 0.00000 SCALE2 0.000000 0.066519 -0.000801 0.00000 SCALE3 0.000000 0.000000 0.105172 0.00000 MASTER 257 0 0 0 0 0 0 6 84 2 0 2 END