HEADER DNA 04-DEC-22 8FDR TITLE STRUCTURE OF A DODECAMER COMPLEX: 5'-CGCGAAAAGCCG-3-DB1476 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*TP*TP*TP*TP*CP*GP*CP*G)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606 KEYWDS DNA, AT SEQUENCE, MINOR GROOVE EXPDTA X-RAY DIFFRACTION AUTHOR E.OGBONNA,W.D.WILSON REVDAT 2 30-AUG-23 8FDR 1 JRNL REVDAT 1 22-FEB-23 8FDR 0 JRNL AUTH E.N.OGBONNA,A.PAUL,A.A.FARAHAT,J.R.TERRELL,E.MINEVA, JRNL AUTH 2 V.OGBONNA,D.W.BOYKIN,W.D.WILSON JRNL TITL X-RAY STRUCTURE CHARACTERIZATION OF THE SELECTIVE JRNL TITL 2 RECOGNITION OF AT BASE PAIR SEQUENCES. JRNL REF ACS BIO MED CHEM AU V. 3 335 2023 JRNL REFN ESSN 2694-2437 JRNL PMID 37599788 JRNL DOI 10.1021/ACSBIOMEDCHEMAU.3C00002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.N.OGBONNA,A.PAUL,A.FAHARAT,J.R.TERRELL,V.OGBONNA, REMARK 1 AUTH 2 D.W.BOYKIN,W.D.WILSON REMARK 1 TITL X-RAY STRUCTURE CHARACTERIZATION OF THE SELECTIVE REMARK 1 TITL 2 RECOGNITION OF AT BASE PAIR SEQUENCES REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 10392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1040 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 25.5200 - 2.9700 0.99 1429 159 0.1819 0.2054 REMARK 3 2 2.9600 - 2.3500 1.00 1353 150 0.2795 0.2882 REMARK 3 3 2.3500 - 2.0600 1.00 1344 150 0.2427 0.2637 REMARK 3 4 2.0600 - 1.8700 1.00 1331 148 0.2575 0.3382 REMARK 3 5 1.8700 - 1.7300 1.00 1306 146 0.2351 0.2780 REMARK 3 6 1.7300 - 1.6300 0.98 1287 142 0.2660 0.3210 REMARK 3 7 1.6300 - 1.5500 0.99 1302 145 0.2964 0.3069 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) : 0.146 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.365 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.20 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 : 0.010 574 REMARK 3 ANGLE : 1.289 879 REMARK 3 CHIRALITY : 0.065 94 REMARK 3 PLANARITY : 0.015 29 REMARK 3 DIHEDRAL : 29.552 258 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 15.0772 20.7722 8.8244 REMARK 3 T TENSOR REMARK 3 T11: 0.2614 T22: 0.2416 REMARK 3 T33: 0.2354 T12: -0.0075 REMARK 3 T13: 0.0163 T23: -0.0146 REMARK 3 L TENSOR REMARK 3 L11: 0.2352 L22: 0.7361 REMARK 3 L33: 5.0564 L12: -0.0062 REMARK 3 L13: 0.5623 L23: 1.4044 REMARK 3 S TENSOR REMARK 3 S11: 0.1422 S12: -0.0497 S13: 0.0211 REMARK 3 S21: -0.1407 S22: 0.1293 S23: -0.1750 REMARK 3 S31: -0.3735 S32: -0.0487 S33: -0.2970 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 8FDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270473. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 104344 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 25.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM CACODYLATE TRIHYDRATE, REMARK 280 SPERMINE TETRACHLORIDE, SODIUM CHLORIDE, MAGNESIUM HEXAHYDRATE, REMARK 280 PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 12.88050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.23450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.92000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.23450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.88050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.92000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OP1 DG C 14 O HOH C 101 1.83 REMARK 500 O HOH B 239 O HOH B 242 2.12 REMARK 500 N7 DA B 7 O HOH B 201 2.14 REMARK 500 O HOH B 218 O HOH C 118 2.19 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 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 208 O REMARK 620 2 HOH B 211 O 89.2 REMARK 620 3 HOH B 216 O 87.0 89.3 REMARK 620 4 HOH B 219 O 177.7 91.4 95.3 REMARK 620 5 HOH B 223 O 84.2 170.9 84.2 95.5 REMARK 620 6 HOH C 113 O 88.8 97.0 172.3 88.9 89.0 REMARK 620 N 1 2 3 4 5 DBREF 8FDR B 1 12 PDB 8FDR 8FDR 1 12 DBREF 8FDR C 13 24 PDB 8FDR 8FDR 13 24 SEQRES 1 B 12 DC DG DC DG DA DA DA DA DC DG DC DG SEQRES 1 C 12 DC DG DC DG DT DT DT DT DC DG DC DG HET WFB B 101 45 HET MG B 102 1 HETNAM WFB 4,4'-(1H-BENZIMIDAZOLE-2,6-DIYL)DI(BENZENE-1- HETNAM 2 WFB CARBOXIMIDAMIDE) HETNAM MG MAGNESIUM ION FORMUL 3 WFB C21 H18 N6 FORMUL 4 MG MG 2+ FORMUL 5 HOH *75(H2 O) LINK MG MG B 102 O HOH B 208 1555 3645 2.18 LINK MG MG B 102 O HOH B 211 1555 3645 2.16 LINK MG MG B 102 O HOH B 216 1555 1555 2.07 LINK MG MG B 102 O HOH B 219 1555 1555 2.01 LINK MG MG B 102 O HOH B 223 1555 1555 2.19 LINK MG MG B 102 O HOH C 113 1555 3645 2.11 CRYST1 25.761 39.840 66.469 90.00 90.00 90.00 P 21 21 21 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 0.038818 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025100 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015045 0.00000