HEADER DNA 18-AUG-25 9Q3B TITLE [21-6B G|A] 21 BP DNA ASSEMBLY THAT PROPAGATES VIA BLUNT-END STACKING TITLE 2 WITH G STACKING ON A AT THE INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*AP*CP*AP*GP*CP*CP*TP*GP*TP*CP*GP*GP*AP*CP*AP*TP*CP*AP*GP*A)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*CP*CP*GP*AP*CP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*GP*GP*CP*TP*GP*TP*C)-3'); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS DNA, TRIGONAL, TENSEGRITY EXPDTA X-RAY DIFFRACTION AUTHOR A.HORVATH,K.WOLOSZYN,S.VECCHIONI,Y.P.OHAYON,R.SHA REVDAT 1 05-NOV-25 9Q3B 0 JRNL AUTH A.HORVATH,K.WOLOSZYN,S.VECCHIONI,Y.P.OHAYON,R.SHA JRNL TITL BLUNTED TENSEGRITY TRIANGLES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 3.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 57.7 REMARK 3 NUMBER OF REFLECTIONS : 1998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 105 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 18.6800 - 3.5500 0.58 1893 105 0.2453 0.2938 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.549 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.631 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 208.1 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 : 0.005 956 REMARK 3 ANGLE : 0.725 1467 REMARK 3 CHIRALITY : 0.035 166 REMARK 3 PLANARITY : 0.003 42 REMARK 3 DIHEDRAL : 37.446 442 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 8) REMARK 3 ORIGIN FOR THE GROUP (A): 38.9352 3.8227 10.7711 REMARK 3 T TENSOR REMARK 3 T11: 3.3905 T22: 0.8789 REMARK 3 T33: 1.9814 T12: -0.4766 REMARK 3 T13: 0.2664 T23: -0.6040 REMARK 3 L TENSOR REMARK 3 L11: 1.3542 L22: -0.0012 REMARK 3 L33: -0.0130 L12: -0.1867 REMARK 3 L13: -0.0393 L23: -0.0478 REMARK 3 S TENSOR REMARK 3 S11: 0.8751 S12: 1.2787 S13: -1.1760 REMARK 3 S21: -4.0730 S22: 1.6875 S23: 0.2443 REMARK 3 S31: -4.0876 S32: 2.1136 S33: 0.1453 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 10 THROUGH 16) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8421 -35.0852 15.2440 REMARK 3 T TENSOR REMARK 3 T11: 3.8163 T22: 1.4550 REMARK 3 T33: 2.6532 T12: -0.8725 REMARK 3 T13: 0.6228 T23: -0.6483 REMARK 3 L TENSOR REMARK 3 L11: 7.9396 L22: 4.8913 REMARK 3 L33: 6.8126 L12: 0.8682 REMARK 3 L13: -5.2291 L23: -4.5778 REMARK 3 S TENSOR REMARK 3 S11: -0.3918 S12: -2.1996 S13: -1.0735 REMARK 3 S21: 0.4516 S22: -1.2734 S23: 1.9808 REMARK 3 S31: -1.1301 S32: 0.6200 S33: 2.1814 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 3 THROUGH 23) REMARK 3 ORIGIN FOR THE GROUP (A): 27.6922 -14.2440 11.9285 REMARK 3 T TENSOR REMARK 3 T11: 2.2041 T22: 1.8512 REMARK 3 T33: 1.6047 T12: -0.2214 REMARK 3 T13: -0.1373 T23: 0.1129 REMARK 3 L TENSOR REMARK 3 L11: 3.3809 L22: 8.6571 REMARK 3 L33: 5.3878 L12: -5.0226 REMARK 3 L13: -3.7712 L23: 6.9061 REMARK 3 S TENSOR REMARK 3 S11: -0.3258 S12: 1.8782 S13: -1.1893 REMARK 3 S21: 1.2976 S22: 1.0991 S23: -1.9948 REMARK 3 S31: 0.5387 S32: -0.8146 S33: -0.1210 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 0 THROUGH 5) REMARK 3 ORIGIN FOR THE GROUP (A): 25.2476 -15.8698 9.2627 REMARK 3 T TENSOR REMARK 3 T11: 1.9072 T22: 1.7341 REMARK 3 T33: 2.8220 T12: -0.9287 REMARK 3 T13: 0.5342 T23: -0.2853 REMARK 3 L TENSOR REMARK 3 L11: 2.3426 L22: 0.9570 REMARK 3 L33: 1.5119 L12: -1.5484 REMARK 3 L13: 2.0167 L23: -1.2263 REMARK 3 S TENSOR REMARK 3 S11: 2.5989 S12: 0.0232 S13: 2.6205 REMARK 3 S21: 1.1420 S22: 1.1060 S23: 1.8590 REMARK 3 S31: 0.3779 S32: -0.8639 S33: -0.7775 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 9Q3B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000298397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92010 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 : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1998 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.545 REMARK 200 RESOLUTION RANGE LOW (A) : 18.682 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.10 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 (%): 78.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MOPS, 1.25 M MAGNESIUM SULFATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.86000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.93000 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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, B, C, D REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 34.50600 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -59.76615 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 35.86000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 69.01200 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 17.93000 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 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 0 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9Q3B A 3 23 PDB 9Q3B 9Q3B 3 23 DBREF 9Q3B B 0 5 PDB 9Q3B 9Q3B 0 5 DBREF 9Q3B C 1 8 PDB 9Q3B 9Q3B 1 8 DBREF 9Q3B D 10 16 PDB 9Q3B 9Q3B 10 16 SEQRES 1 A 21 DG DA DC DA DG DC DC DT DG DT DC DG DG SEQRES 2 A 21 DA DC DA DT DC DA DG DA SEQRES 1 B 6 DC DC DG DA DC DA SEQRES 1 C 8 DT DC DT DG DA DT DG DT SEQRES 1 D 7 DG DG DC DT DG DT DC CRYST1 69.012 69.012 53.790 90.00 90.00 120.00 P 32 3 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 0.014490 0.008366 0.000000 0.00000 SCALE2 0.000000 0.016732 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018591 0.00000 MASTER 272 0 0 0 0 0 0 6 855 4 0 5 END