HEADER PROTEIN FIBRIL 09-JAN-20 6VHC TITLE 1.4A DAMAGED STRUCTURE OF GSNQNNF USED TO DETERMINE INITIAL PHASES TITLE 2 FROM RADIATION DAMAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GSNQNNF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS MICROED, DAMAGE, PHASING, RIP, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR M.W.MARTYNOWYCZ,J.HATTNE,T.GONEN REVDAT 3 06-MAR-24 6VHC 1 REMARK LINK REVDAT 2 22-APR-20 6VHC 1 JRNL REVDAT 1 19-FEB-20 6VHC 0 JRNL AUTH M.W.MARTYNOWYCZ,J.HATTNE,T.GONEN JRNL TITL EXPERIMENTAL PHASING OF MICROED DATA USING RADIATION DAMAGE. JRNL REF STRUCTURE V. 28 458 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 32023481 JRNL DOI 10.1016/J.STR.2020.01.008 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 78.1 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RCOMPLETE RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 55 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VHC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246395. 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 : 722 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 78.1 REMARK 240 DATA REDUNDANCY : 8.745 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.40 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.51 REMARK 240 COMPLETENESS FOR SHELL (%) : 79.0 REMARK 240 DATA REDUNDANCY IN SHELL : 9.38 REMARK 240 R MERGE FOR SHELL (I) : 0.27200 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: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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: MONOMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 7 C PHE A 7 OXT 0.154 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 1 N REMARK 620 2 GLY A 1 O 82.6 REMARK 620 3 PHE A 7 O 115.8 47.1 REMARK 620 4 ACT A 102 OXT 140.3 85.2 80.8 REMARK 620 5 ACT A 102 O 112.0 91.6 49.4 106.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6CLJ RELATED DB: PDB REMARK 900 DAMAGED DATASET REFINED TO 1.4A REMARK 900 RELATED ID: EMD-21203 RELATED DB: EMDB REMARK 900 1.4A DAMAGED STRUCTURE OF GSNQNNF USED TO DETERMINE INITIAL PHASES REMARK 900 FROM RADIATION DAMAGE DBREF 6VHC A 1 7 PDB 6VHC 6VHC 1 7 SEQRES 1 A 7 GLY SER ASN GLN ASN ASN PHE HET ZN A 101 1 HET ACT A 102 4 HETNAM ZN ZINC ION HETNAM ACT ACETATE ION FORMUL 2 ZN ZN 2+ FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *(H2 O) LINK N GLY A 1 ZN ZN A 101 1555 1555 2.09 LINK O GLY A 1 ZN ZN A 101 1555 1555 1.90 LINK O PHE A 7 ZN ZN A 101 1555 1644 1.93 LINK ZN ZN A 101 OXT ACT A 102 1555 1555 1.93 LINK ZN ZN A 101 O ACT A 102 1555 1655 1.85 SITE 1 AC1 2 GLY A 1 ACT A 102 SITE 1 AC2 2 GLY A 1 ZN A 101 CRYST1 4.880 14.170 17.620 83.60 84.98 83.31 P 1 1 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 0.204918 -0.024036 -0.015622 0.00000 SCALE2 0.000000 0.071055 -0.007312 0.00000 SCALE3 0.000000 0.000000 0.057273 0.00000 ATOM 1 N GLY A 1 3.352 30.635 19.446 1.00 2.54 N ATOM 2 CA GLY A 1 3.582 30.781 18.001 1.00 3.05 C ATOM 3 C GLY A 1 2.722 29.748 17.239 1.00 2.15 C ATOM 4 O GLY A 1 2.048 28.961 17.880 1.00 5.81 O ATOM 5 N SER A 2 2.815 29.826 15.911 1.00 0.08 N ATOM 6 CA SER A 2 1.966 29.000 15.044 1.00 3.15 C ATOM 7 C SER A 2 2.692 27.766 14.535 1.00 2.17 C ATOM 8 O SER A 2 3.936 27.724 14.410 1.00 10.36 O ATOM 9 CB SER A 2 1.497 29.894 13.888 1.00 0.87 C ATOM 10 OG SER A 2 0.537 30.854 14.311 1.00 5.15 O ATOM 11 N ASN A 3 1.976 26.681 14.230 1.00 4.06 N ATOM 12 CA ASN A 3 2.586 25.396 13.846 1.00 4.92 C ATOM 13 C ASN A 3 1.937 24.842 12.580 1.00 6.01 C ATOM 14 O ASN A 3 0.707 24.877 12.436 1.00 6.39 O ATOM 15 CB ASN A 3 2.488 24.407 15.003 1.00 2.71 C ATOM 16 CG ASN A 3 3.104 24.964 16.280 1.00 7.61 C ATOM 17 OD1 ASN A 3 4.288 24.750 16.541 1.00 13.01 O ATOM 18 ND2 ASN A 3 2.309 25.698 17.061 1.00 6.41 N ATOM 19 N GLN A 4 2.705 24.292 11.640 1.00 6.60 N ATOM 20 CA GLN A 4 2.182 23.569 10.488 1.00 1.91 C ATOM 21 C GLN A 4 2.863 22.213 10.363 1.00 3.23 C ATOM 22 O GLN A 4 4.108 22.094 10.478 1.00 0.08 O ATOM 23 CB GLN A 4 2.392 24.378 9.209 1.00 8.50 C ATOM 24 CG GLN A 4 1.649 23.895 7.969 1.00 1.46 C ATOM 25 CD GLN A 4 2.004 24.719 6.757 1.00 6.42 C ATOM 26 OE1 GLN A 4 3.210 24.746 6.457 1.00 7.39 O ATOM 27 NE2 GLN A 4 1.080 25.369 6.068 1.00 2.55 N ATOM 28 N ASN A 5 2.123 21.139 10.147 1.00 2.03 N ATOM 29 CA ASN A 5 2.658 19.825 9.794 1.00 3.92 C ATOM 30 C ASN A 5 2.265 19.502 8.360 1.00 0.44 C ATOM 31 O ASN A 5 1.063 19.505 8.063 1.00 5.87 O ATOM 32 CB ASN A 5 2.159 18.767 10.767 1.00 7.76 C ATOM 33 CG ASN A 5 2.607 18.979 12.196 1.00 6.12 C ATOM 34 OD1 ASN A 5 3.823 18.881 12.442 1.00 7.88 O ATOM 35 ND2 ASN A 5 1.764 19.270 13.168 1.00 5.96 N ATOM 36 N ASN A 6 3.232 19.248 7.487 1.00 6.82 N ATOM 37 CA ASN A 6 2.945 18.815 6.125 1.00 0.76 C ATOM 38 C ASN A 6 3.439 17.379 5.971 1.00 0.71 C ATOM 39 O ASN A 6 4.610 17.126 5.684 1.00 2.63 O ATOM 40 CB ASN A 6 3.585 19.707 5.054 1.00 0.15 C ATOM 41 CG ASN A 6 3.286 21.173 5.370 1.00 2.53 C ATOM 42 OD1 ASN A 6 4.187 21.966 5.690 1.00 0.08 O ATOM 43 ND2 ASN A 6 2.036 21.574 5.286 1.00 6.63 N ATOM 44 N PHE A 7 2.582 16.385 6.146 1.00 0.45 N ATOM 45 CA PHE A 7 2.917 14.989 5.910 1.00 2.51 C ATOM 46 C PHE A 7 3.048 14.693 4.429 1.00 2.55 C ATOM 47 O PHE A 7 3.652 13.623 4.121 1.00 8.65 O ATOM 48 CB PHE A 7 1.829 14.131 6.567 1.00 0.08 C ATOM 49 CG PHE A 7 1.843 14.245 8.075 1.00 3.09 C ATOM 50 CD1 PHE A 7 2.677 13.488 8.866 1.00 0.08 C ATOM 51 CD2 PHE A 7 1.022 15.156 8.742 1.00 1.30 C ATOM 52 CE1 PHE A 7 2.725 13.498 10.235 1.00 0.08 C ATOM 53 CE2 PHE A 7 1.048 15.210 10.125 1.00 0.08 C ATOM 54 CZ PHE A 7 1.920 14.442 10.882 1.00 7.52 C ATOM 55 OXT PHE A 7 2.698 15.281 3.227 1.00 9.97 O TER 56 PHE A 7 HETATM 57 ZN ZN A 101 2.231 28.897 19.765 1.00 5.28 ZN HETATM 58 C ACT A 102 -0.360 27.290 19.888 1.00 18.27 C HETATM 59 O ACT A 102 -1.604 27.369 19.663 1.00 10.70 O HETATM 60 OXT ACT A 102 0.396 28.290 19.760 1.00 0.85 O HETATM 61 CH3 ACT A 102 0.255 25.939 20.324 1.00 8.80 C HETATM 62 O HOH A 201 1.048 17.801 3.043 1.00 9.89 O CONECT 1 57 CONECT 4 57 CONECT 57 1 4 60 CONECT 58 59 60 61 CONECT 59 58 CONECT 60 57 58 CONECT 61 58 MASTER 184 0 2 0 0 0 2 6 61 1 7 1 END