HEADER PROTEIN FIBRIL 28-MAY-21 7N2D TITLE MICROED STRUCTURE OF HUMAN ZINC FINGER PROTEIN 292 SEGMENT (534-542) TITLE 2 PHASED BY ARCIMBOLDO-BORGES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN 292; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 534-542; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, MICROED, ZINC FINGER, PHASING, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR L.S.RICHARDS,M.D.FLORES,C.T.ZEE,C.GLYNN,M.GALLAGHER-JONES,M.R.SAWAYA REVDAT 3 22-MAY-24 7N2D 1 REMARK REVDAT 2 10-MAY-23 7N2D 1 JRNL REVDAT 1 01-JUN-22 7N2D 0 JRNL AUTH L.S.RICHARDS,M.D.FLORES,C.MILLAN,C.GLYNN,C.T.ZEE,M.R.SAWAYA, JRNL AUTH 2 M.GALLAGHER-JONES,R.J.BORGES,I.USON,J.A.RODRIGUEZ JRNL TITL FRAGMENT-BASED AB INITIO PHASING OF PEPTIDIC NANOCRYSTALS BY JRNL TITL 2 MICROED. JRNL REF ACS BIO MED CHEM AU V. 3 201 2023 JRNL REFN ESSN 2694-2437 JRNL PMID 37096030 JRNL DOI 10.1021/ACSBIOMEDCHEMAU.2C00082 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 76.8 REMARK 3 NUMBER OF REFLECTIONS : 961 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 96 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.3890 - 2.7295 0.88 187 21 0.1894 0.1639 REMARK 3 2 2.7295 - 2.1674 0.90 171 19 0.1789 0.2732 REMARK 3 3 2.1674 - 1.8937 0.92 173 19 0.1812 0.2927 REMARK 3 4 1.8937 - 1.7206 0.82 139 16 0.2565 0.2994 REMARK 3 5 1.7206 - 1.5974 0.55 92 10 0.2829 0.3963 REMARK 3 6 1.5974 - 1.5032 0.52 103 11 0.3672 0.4451 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7N2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000254642. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : FILAMENT 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 : 961 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 240 RESOLUTION RANGE LOW (A) : 19.389 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 75.8 REMARK 240 DATA REDUNDANCY : 4.180 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.50 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.60 REMARK 240 COMPLETENESS FOR SHELL (%) : 51.1 REMARK 240 DATA REDUNDANCY IN SHELL : 2.73 REMARK 240 R MERGE FOR SHELL (I) : 0.43600 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 21.56000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.56000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.42000 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL 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: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 2 72.24 61.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 7N2D A 0 8 PDB 7N2D 7N2D 0 8 SEQRES 1 A 9 PHE ARG ASN TRP GLN ALA TYR MET GLN HET DMS A 101 4 HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 DMS C2 H6 O S FORMUL 3 HOH *2(H2 O) CRYST1 43.120 4.840 34.900 90.00 115.93 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 0.023191 0.000000 0.011278 0.00000 SCALE2 0.000000 0.206612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031862 0.00000 ATOM 1 N PHE A 0 19.498 -1.818 3.442 1.00 10.87 N ATOM 2 CA PHE A 0 20.157 -1.009 4.469 1.00 9.58 C ATOM 3 C PHE A 0 21.272 -1.775 5.192 1.00 9.09 C ATOM 4 O PHE A 0 21.341 -3.003 5.112 1.00 8.34 O ATOM 5 CB PHE A 0 19.126 -0.513 5.481 1.00 13.59 C ATOM 6 CG PHE A 0 18.433 -1.609 6.252 1.00 11.05 C ATOM 7 CD1 PHE A 0 18.918 -2.023 7.485 1.00 9.04 C ATOM 8 CD2 PHE A 0 17.256 -2.180 5.773 1.00 15.45 C ATOM 9 CE1 PHE A 0 18.269 -3.022 8.210 1.00 21.97 C ATOM 10 CE2 PHE A 0 16.602 -3.173 6.492 1.00 12.12 C ATOM 11 CZ PHE A 0 17.101 -3.593 7.717 1.00 7.25 C ATOM 12 N ARG A 1 22.161 -1.058 5.886 1.00 8.22 N ATOM 13 CA ARG A 1 23.199 -1.699 6.685 1.00 6.63 C ATOM 14 C ARG A 1 23.431 -0.906 7.963 1.00 3.89 C ATOM 15 O ARG A 1 23.319 0.319 7.961 1.00 6.06 O ATOM 16 CB ARG A 1 24.507 -1.815 5.920 1.00 11.80 C ATOM 17 CG ARG A 1 24.422 -2.785 4.740 1.00 10.99 C ATOM 18 CD ARG A 1 25.722 -2.794 3.958 1.00 14.43 C ATOM 19 NE ARG A 1 25.609 -3.594 2.738 1.00 9.42 N ATOM 20 CZ ARG A 1 26.520 -3.614 1.768 1.00 10.21 C ATOM 21 NH1 ARG A 1 26.316 -4.366 0.686 1.00 6.26 N ATOM 22 NH2 ARG A 1 27.638 -2.889 1.868 1.00 9.62 N ATOM 23 N ASN A 2 23.794 -1.610 9.034 1.00 6.86 N ATOM 24 CA ASN A 2 24.050 -1.009 10.346 1.00 9.43 C ATOM 25 C ASN A 2 22.793 -0.310 10.888 1.00 8.01 C ATOM 26 O ASN A 2 22.683 0.921 10.921 1.00 5.35 O ATOM 27 CB ASN A 2 25.235 -0.024 10.288 1.00 5.97 C ATOM 28 CG ASN A 2 26.603 -0.705 10.455 1.00 2.96 C ATOM 29 OD1 ASN A 2 26.716 -1.916 10.400 1.00 5.56 O ATOM 30 ND2 ASN A 2 27.635 0.094 10.678 1.00 8.35 N ATOM 31 N TRP A 3 21.827 -1.138 11.293 1.00 8.35 N ATOM 32 CA TRP A 3 20.652 -0.716 12.043 1.00 5.47 C ATOM 33 C TRP A 3 20.833 -1.227 13.469 1.00 3.56 C ATOM 34 O TRP A 3 21.050 -2.426 13.672 1.00 6.24 O ATOM 35 CB TRP A 3 19.380 -1.288 11.401 1.00 7.04 C ATOM 36 CG TRP A 3 18.077 -0.839 11.982 1.00 12.17 C ATOM 37 CD1 TRP A 3 17.237 0.115 11.467 1.00 15.97 C ATOM 38 CD2 TRP A 3 17.438 -1.331 13.175 1.00 8.14 C ATOM 39 NE1 TRP A 3 16.119 0.246 12.265 1.00 13.34 N ATOM 40 CE2 TRP A 3 16.216 -0.633 13.313 1.00 7.76 C ATOM 41 CE3 TRP A 3 17.769 -2.307 14.127 1.00 8.92 C ATOM 42 CZ2 TRP A 3 15.335 -0.860 14.385 1.00 7.81 C ATOM 43 CZ3 TRP A 3 16.899 -2.527 15.190 1.00 8.96 C ATOM 44 CH2 TRP A 3 15.691 -1.815 15.303 1.00 6.95 C ATOM 45 N GLN A 4 20.748 -0.336 14.446 1.00 2.62 N ATOM 46 CA GLN A 4 21.117 -0.686 15.819 1.00 2.28 C ATOM 47 C GLN A 4 20.172 -0.014 16.790 1.00 3.87 C ATOM 48 O GLN A 4 20.031 1.210 16.762 1.00 2.90 O ATOM 49 CB GLN A 4 22.574 -0.270 16.126 1.00 5.43 C ATOM 50 CG GLN A 4 23.016 -0.412 17.596 1.00 4.69 C ATOM 51 CD GLN A 4 24.449 0.098 17.819 1.00 4.33 C ATOM 52 OE1 GLN A 4 24.667 1.292 17.961 1.00 3.14 O ATOM 53 NE2 GLN A 4 25.428 -0.817 17.844 1.00 5.41 N ATOM 54 N ALA A 5 19.573 -0.801 17.680 1.00 6.06 N ATOM 55 CA ALA A 5 18.629 -0.268 18.644 1.00 4.71 C ATOM 56 C ALA A 5 18.805 -0.953 19.983 1.00 3.05 C ATOM 57 O ALA A 5 19.041 -2.160 20.043 1.00 8.93 O ATOM 58 CB ALA A 5 17.184 -0.449 18.175 1.00 8.33 C ATOM 59 N TYR A 6 18.650 -0.172 21.043 1.00 4.12 N ATOM 60 CA TYR A 6 18.644 -0.676 22.413 1.00 4.86 C ATOM 61 C TYR A 6 17.397 -0.104 23.064 1.00 11.54 C ATOM 62 O TYR A 6 17.235 1.120 23.107 1.00 8.92 O ATOM 63 CB TYR A 6 19.910 -0.252 23.170 1.00 10.24 C ATOM 64 CG TYR A 6 20.107 -0.973 24.485 1.00 9.58 C ATOM 65 CD1 TYR A 6 19.291 -0.696 25.580 1.00 7.40 C ATOM 66 CD2 TYR A 6 21.099 -1.939 24.627 1.00 7.65 C ATOM 67 CE1 TYR A 6 19.449 -1.358 26.785 1.00 10.80 C ATOM 68 CE2 TYR A 6 21.263 -2.614 25.824 1.00 11.89 C ATOM 69 CZ TYR A 6 20.439 -2.319 26.901 1.00 6.75 C ATOM 70 OH TYR A 6 20.597 -2.986 28.089 1.00 9.14 O ATOM 71 N MET A 7 16.493 -0.974 23.523 1.00 8.15 N ATOM 72 CA AMET A 7 15.293 -0.499 24.191 0.50 10.84 C ATOM 73 CA BMET A 7 15.233 -0.578 24.150 0.50 10.90 C ATOM 74 C MET A 7 15.163 -1.130 25.566 1.00 7.74 C ATOM 75 O MET A 7 15.470 -2.303 25.777 1.00 8.29 O ATOM 76 CB AMET A 7 14.021 -0.757 23.373 0.50 12.62 C ATOM 77 CB BMET A 7 14.016 -1.119 23.377 0.50 12.83 C ATOM 78 CG AMET A 7 13.886 -2.134 22.801 0.50 13.81 C ATOM 79 CG BMET A 7 13.706 -0.427 22.082 0.50 20.26 C ATOM 80 SD AMET A 7 12.992 -2.045 21.244 0.50 10.30 S ATOM 81 SD BMET A 7 14.911 -0.800 20.806 0.50 9.79 S ATOM 82 CE AMET A 7 14.364 -1.712 20.133 0.50 12.27 C ATOM 83 CE BMET A 7 14.348 -2.378 20.212 0.50 9.11 C ATOM 84 N GLN A 8 14.712 -0.314 26.510 1.00 4.22 N ATOM 85 CA GLN A 8 14.488 -0.787 27.869 1.00 8.12 C ATOM 86 C GLN A 8 13.356 0.029 28.499 1.00 18.68 C ATOM 87 O GLN A 8 12.941 -0.200 29.634 1.00 19.77 O ATOM 88 CB GLN A 8 15.774 -0.701 28.699 1.00 9.11 C ATOM 89 CG GLN A 8 16.280 0.691 28.982 1.00 11.64 C ATOM 90 CD GLN A 8 17.631 0.702 29.688 1.00 10.55 C ATOM 91 OE1 GLN A 8 18.018 -0.272 30.351 1.00 8.52 O ATOM 92 NE2 GLN A 8 18.365 1.802 29.540 1.00 13.25 N ATOM 93 OXT GLN A 8 12.812 0.939 27.879 1.00 11.69 O TER 94 GLN A 8 HETATM 95 S DMS A 101 22.707 -0.966 1.240 1.00 31.59 S HETATM 96 O DMS A 101 23.179 -0.258 2.466 1.00 29.95 O HETATM 97 C1 DMS A 101 24.099 -1.725 0.366 1.00 29.08 C HETATM 98 C2 DMS A 101 21.877 -2.493 1.715 1.00 23.85 C HETATM 99 O HOH A 201 13.407 -2.447 30.666 1.00 11.91 O HETATM 100 O HOH A 202 18.081 -4.112 2.483 1.00 19.88 O CONECT 95 96 97 98 CONECT 96 95 CONECT 97 95 CONECT 98 95 MASTER 187 0 1 0 0 0 0 6 94 1 4 1 END