HEADER PROTEIN FIBRIL 09-JAN-20 6VHB TITLE 1.4A LOW-DOSE STRUCTURE OF GSNQNNF DETERMINED FROM INITIAL PHASES TITLE 2 GENERATED USING 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 6VHB 1 REMARK LINK REVDAT 2 22-APR-20 6VHB 1 JRNL REVDAT 1 19-FEB-20 6VHB 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) : 14.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 77.2 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 6VHB 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_1000246394. 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 : 713 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 (%) : 77.2 REMARK 240 DATA REDUNDANCY : 8.452 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 (%) : 78.5 REMARK 240 DATA REDUNDANCY IN SHELL : 8.55 REMARK 240 R MERGE FOR SHELL (I) : 0.26200 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 ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 PHE A 7 CG - CD1 - CE1 ANGL. DEV. = 6.9 DEGREES 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 85.4 REMARK 620 3 PHE A 7 O 115.0 45.1 REMARK 620 4 ACT A 102 O 146.1 87.4 81.3 REMARK 620 5 ACT A 102 OXT 115.7 97.3 54.5 98.0 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: 6CLI RELATED DB: PDB REMARK 900 ORIGINAL STRUCTURE REMARK 900 RELATED ID: EMD-21202 RELATED DB: EMDB REMARK 900 1.4A LOW-DOSE STRUCTURE OF GSNQNNF DETERMINED FROM INITIAL PHASES REMARK 900 GENERATED USING RADIATION DAMAGE DBREF 6VHB A 1 7 PDB 6VHB 6VHB 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 1.98 LINK O GLY A 1 ZN ZN A 101 1555 1555 1.86 LINK O PHE A 7 ZN ZN A 101 1555 1644 2.09 LINK ZN ZN A 101 O ACT A 102 1555 1555 2.05 LINK ZN ZN A 101 OXT ACT A 102 1555 1655 2.03 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 3.399 30.601 19.375 1.00 0.93 N ATOM 2 CA GLY A 1 3.623 30.787 17.936 1.00 2.92 C ATOM 3 C GLY A 1 2.760 29.752 17.177 1.00 2.30 C ATOM 4 O GLY A 1 2.082 28.974 17.829 1.00 1.80 O ATOM 5 N SER A 2 2.858 29.801 15.858 1.00 0.08 N ATOM 6 CA SER A 2 1.978 28.995 15.000 1.00 0.69 C ATOM 7 C SER A 2 2.692 27.753 14.486 1.00 0.08 C ATOM 8 O SER A 2 3.941 27.738 14.345 1.00 5.90 O ATOM 9 CB SER A 2 1.496 29.908 13.854 1.00 0.08 C ATOM 10 OG SER A 2 0.525 30.854 14.292 1.00 1.15 O ATOM 11 N ASN A 3 2.001 26.639 14.227 1.00 3.22 N ATOM 12 CA ASN A 3 2.564 25.333 13.879 1.00 0.71 C ATOM 13 C ASN A 3 1.886 24.766 12.635 1.00 5.01 C ATOM 14 O ASN A 3 0.664 24.755 12.452 1.00 2.18 O ATOM 15 CB ASN A 3 2.476 24.373 15.080 1.00 1.83 C ATOM 16 CG ASN A 3 3.085 24.989 16.330 1.00 2.00 C ATOM 17 OD1 ASN A 3 4.269 24.769 16.627 1.00 9.96 O ATOM 18 ND2 ASN A 3 2.316 25.785 17.055 1.00 5.13 N ATOM 19 N GLN A 4 2.678 24.238 11.700 1.00 4.45 N ATOM 20 CA GLN A 4 2.184 23.550 10.509 1.00 3.39 C ATOM 21 C GLN A 4 2.899 22.223 10.328 1.00 2.04 C ATOM 22 O GLN A 4 4.140 22.071 10.430 1.00 0.12 O ATOM 23 CB GLN A 4 2.369 24.421 9.272 1.00 6.63 C ATOM 24 CG GLN A 4 1.691 23.888 8.022 1.00 1.39 C ATOM 25 CD GLN A 4 1.991 24.745 6.803 1.00 4.34 C ATOM 26 OE1 GLN A 4 3.183 24.831 6.461 1.00 3.23 O ATOM 27 NE2 GLN A 4 1.043 25.357 6.123 1.00 0.45 N ATOM 28 N ASN A 5 2.112 21.173 10.084 1.00 0.09 N ATOM 29 CA ASN A 5 2.651 19.846 9.815 1.00 2.42 C ATOM 30 C ASN A 5 2.254 19.479 8.384 1.00 0.08 C ATOM 31 O ASN A 5 1.039 19.403 8.168 1.00 2.03 O ATOM 32 CB ASN A 5 2.134 18.813 10.809 1.00 3.76 C ATOM 33 CG ASN A 5 2.548 18.996 12.249 1.00 3.78 C ATOM 34 OD1 ASN A 5 3.731 18.787 12.574 1.00 6.41 O ATOM 35 ND2 ASN A 5 1.663 19.359 13.159 1.00 6.64 N ATOM 36 N ASN A 6 3.197 19.266 7.485 1.00 5.08 N ATOM 37 CA ASN A 6 2.922 18.857 6.113 1.00 0.40 C ATOM 38 C ASN A 6 3.395 17.427 5.919 1.00 0.08 C ATOM 39 O ASN A 6 4.578 17.213 5.622 1.00 0.08 O ATOM 40 CB ASN A 6 3.595 19.774 5.086 1.00 0.71 C ATOM 41 CG ASN A 6 3.264 21.223 5.407 1.00 1.54 C ATOM 42 OD1 ASN A 6 4.162 22.031 5.685 1.00 0.08 O ATOM 43 ND2 ASN A 6 1.990 21.560 5.360 1.00 6.19 N ATOM 44 N PHE A 7 2.564 16.413 6.100 1.00 0.08 N ATOM 45 CA PHE A 7 2.941 15.023 5.907 1.00 0.08 C ATOM 46 C PHE A 7 3.109 14.697 4.440 1.00 0.79 C ATOM 47 O PHE A 7 3.786 13.632 4.230 1.00 5.35 O ATOM 48 CB PHE A 7 1.846 14.141 6.527 1.00 0.08 C ATOM 49 CG PHE A 7 1.860 14.227 8.026 1.00 0.90 C ATOM 50 CD1 PHE A 7 2.665 13.471 8.827 1.00 0.08 C ATOM 51 CD2 PHE A 7 1.035 15.165 8.667 1.00 1.31 C ATOM 52 CE1 PHE A 7 2.732 13.481 10.201 1.00 0.08 C ATOM 53 CE2 PHE A 7 1.073 15.196 10.044 1.00 0.08 C ATOM 54 CZ PHE A 7 1.913 14.429 10.837 1.00 4.13 C ATOM 55 OXT PHE A 7 2.697 15.269 3.478 1.00 3.61 O TER 56 PHE A 7 HETATM 57 ZN ZN A 101 2.274 28.998 19.674 1.00 3.34 ZN HETATM 58 C ACT A 102 -0.344 27.222 20.022 1.00 9.18 C HETATM 59 O ACT A 102 0.367 28.256 19.789 1.00 0.08 O HETATM 60 OXT ACT A 102 -1.608 27.244 19.853 1.00 4.95 O HETATM 61 CH3 ACT A 102 0.296 25.894 20.494 1.00 4.49 C HETATM 62 O HOH A 201 5.941 17.825 3.335 1.00 6.22 O CONECT 1 57 CONECT 4 57 CONECT 57 1 4 59 CONECT 58 59 60 61 CONECT 59 57 58 CONECT 60 58 CONECT 61 58 MASTER 184 0 2 0 0 0 2 6 61 1 7 1 END