HEADER DNA 19-JAN-26 10HF TITLE [17,17,7-7N_3T] ISOSCELES TENSEGRITY TRIANGLE WITH 17, 17 AND 7 BASE TITLE 2 PAIRS BETWEEN JUNCTIONS, THREE TURN EDGES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (31-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*TP*GP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*AP*CP*TP*CP*AP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (31-MER); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA (5'-D(*TP*TP*CP*GP*TP*AP*GP*TP*GP*GP*TP*CP*GP*C)-3'); COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 5; COMPND 19 MOLECULE: DNA (31-MER); COMPND 20 CHAIN: E; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 6; COMPND 23 MOLECULE: DNA (5'- COMPND 24 D(*TP*CP*AP*GP*CP*TP*CP*AP*CP*TP*CP*GP*TP*GP*GP*TP*AP*TP*C)-3'); COMPND 25 CHAIN: F; COMPND 26 ENGINEERED: YES; COMPND 27 MOL_ID: 7; COMPND 28 MOLECULE: DNA (41-MER); COMPND 29 CHAIN: G; COMPND 30 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; SOURCE 17 MOL_ID: 5; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630; SOURCE 21 MOL_ID: 6; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630; SOURCE 25 MOL_ID: 7; SOURCE 26 SYNTHETIC: YES; SOURCE 27 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 28 ORGANISM_TAXID: 32630 KEYWDS TENSEGRITY TRIANGLE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.VECCHIONI,K.WOLOSZYN,R.SHA,Y.P.OHAYON REVDAT 1 25-MAR-26 10HF 0 JRNL AUTH S.VECCHIONI,K.WOLOSZYN,R.SHA,Y.P.OHAYON,L.PERREN JRNL TITL SHAPE ANISOTROPY IN 3D DNA ARCHITECTURES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 7.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 7.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 58.1 REMARK 3 NUMBER OF REFLECTIONS : 2373 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 125 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 44.4700 - 7.2400 0.58 2248 125 0.1416 0.1619 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) : 0.627 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : -1.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 426.1 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 4250 REMARK 3 ANGLE : 0.797 6547 REMARK 3 CHIRALITY : 0.043 737 REMARK 3 PLANARITY : 0.005 186 REMARK 3 DIHEDRAL : 36.793 1832 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): -4.9704 -43.0060 -18.3851 REMARK 3 T TENSOR REMARK 3 T11: 2.7749 T22: 3.5269 REMARK 3 T33: 2.8519 T12: 0.1294 REMARK 3 T13: -0.0883 T23: -0.8025 REMARK 3 L TENSOR REMARK 3 L11: 2.1642 L22: 1.4800 REMARK 3 L33: 6.3412 L12: 0.8252 REMARK 3 L13: 1.3380 L23: -0.1680 REMARK 3 S TENSOR REMARK 3 S11: -0.1333 S12: 2.0753 S13: 0.2721 REMARK 3 S21: 1.2231 S22: 0.1260 S23: 0.4071 REMARK 3 S31: 1.7452 S32: 0.6960 S33: -0.0147 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 10HF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1000303915. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 338-293 AT 0.4/HR 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) : 1.000010 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 : 2402 REMARK 200 RESOLUTION RANGE HIGH (A) : 7.236 REMARK 200 RESOLUTION RANGE LOW (A) : 88.944 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 7.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 8.36 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 (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MOPS, 1.25 M MAGNESIUM SULFATE, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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: HEPTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEPTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G 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 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC A 22 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 23 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC C 30 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC E 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG E 10 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG F 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT F 10 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA G 3 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA G 20 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 10HF A 1 31 PDB 10HF 10HF 1 31 DBREF 10HF B 1 19 PDB 10HF 10HF 1 19 DBREF 10HF C 1 31 PDB 10HF 10HF 1 31 DBREF 10HF D 1 14 PDB 10HF 10HF 1 14 DBREF 10HF E 1 31 PDB 10HF 10HF 1 31 DBREF 10HF F 1 19 PDB 10HF 10HF 1 19 DBREF 10HF G 1 41 PDB 10HF 10HF 1 41 SEQRES 1 A 31 DG DA DC DT DG DA DG DT DC DT DA DC DC SEQRES 2 A 31 DT DG DT DA DC DG DG DA DC DG DA DG DT SEQRES 3 A 31 DG DA DG DC DT SEQRES 1 B 19 DT DG DT DG DA DT DG DT DG DG DT DA DG SEQRES 2 B 19 DA DC DT DC DA DG SEQRES 1 C 31 DA DA DG DA DT DA DC DC DT DG DA DT DA SEQRES 2 C 31 DA DT DA DG DG DT DT DG DA DC DG DG DA SEQRES 3 C 31 DC DT DA DC DG SEQRES 1 D 14 DT DT DC DG DT DA DG DT DG DG DT DC DG SEQRES 2 D 14 DC SEQRES 1 E 31 DC DA DG DC DG DA DC DC DT DG DC DT DC SEQRES 2 E 31 DT DC DG DT DC DT DT DG DT DC DG DG DA SEQRES 3 E 31 DC DA DT DC DA SEQRES 1 F 19 DT DC DA DG DC DT DC DA DC DT DC DG DT SEQRES 2 F 19 DG DG DT DA DT DC SEQRES 1 G 41 DA DC DA DC DC DG DA DC DA DA DG DA DC SEQRES 2 G 41 DG DA DG DA DG DC DA DC DC DG DT DC DA SEQRES 3 G 41 DA DC DC DT DA DT DT DA DT DC DA DC DC SEQRES 4 G 41 DG DT CRYST1 91.665 99.533 100.317 83.09 62.81 66.03 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 0.010909 -0.004850 -0.006013 0.00000 SCALE2 0.000000 0.010995 0.000887 0.00000 SCALE3 0.000000 0.000000 0.011243 0.00000 MASTER 224 0 0 0 0 0 0 6 3792 7 0 19 END