HEADER DNA 18-JAN-26 10FY TITLE [112SE] TWO TURN TENSEGRITY TRIANGLE WITH 1,1 AND 2 BP STICKY ENDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*CP*GP*AP*TP*GP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*AP*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(*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*AP*TP*CP*G)-3'); COMPND 9 CHAIN: E; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*TP*CP*TP*TP*GP*TP*GP*GP*TP*CP*GP*C)-3'); COMPND 13 CHAIN: D; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'- COMPND 17 D(*GP*AP*GP*CP*GP*AP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)- COMPND 18 3'); COMPND 19 CHAIN: B; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*GP*T)- COMPND 23 3'); COMPND 24 CHAIN: F; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: DNA (5'- COMPND 28 D(*AP*AP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)- COMPND 29 3'); COMPND 30 CHAIN: C; COMPND 31 ENGINEERED: YES; COMPND 32 MOL_ID: 7; COMPND 33 MOLECULE: DNA (5'- COMPND 34 D(*AP*CP*AP*CP*CP*GP*AP*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*GP*T)- COMPND 35 3'); COMPND 36 CHAIN: M; COMPND 37 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 10FY 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. 3.90 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) : 3.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 62.2 REMARK 3 NUMBER OF REFLECTIONS : 6767 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 314 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 43.0400 - 4.9200 0.97 5061 210 0.2030 0.2405 REMARK 3 2 4.9200 - 3.9000 0.27 1392 104 0.3355 0.3797 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) : 0.458 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 44.814 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 248.4 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 247.8 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 : 0.007 2870 REMARK 3 ANGLE : 0.985 4417 REMARK 3 CHIRALITY : 0.052 497 REMARK 3 PLANARITY : 0.004 126 REMARK 3 DIHEDRAL : 41.793 1232 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): -2.9526 -4.3383 -5.5541 REMARK 3 T TENSOR REMARK 3 T11: 1.4984 T22: 1.3351 REMARK 3 T33: 1.3757 T12: -0.0844 REMARK 3 T13: -0.1174 T23: -0.1279 REMARK 3 L TENSOR REMARK 3 L11: 3.9034 L22: 4.4216 REMARK 3 L33: 3.4171 L12: -0.5200 REMARK 3 L13: -0.7082 L23: -0.1871 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.3005 S13: -0.6317 REMARK 3 S21: -0.7873 S22: 0.3033 S23: -0.4648 REMARK 3 S31: -0.7488 S32: -0.2842 S33: -0.2151 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 10FY 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_1000304338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 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 : 6774 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.900 REMARK 200 RESOLUTION RANGE LOW (A) : 53.137 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.45 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 : 1.100 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): 8.00 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: 7230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, D, B, F, C, M 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 DC A 102 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 107 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 111 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT E 102 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA E 103 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DA E 103 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG E 104 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DG E 104 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT E 105 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DT E 105 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG E 110 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC D 104 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 105 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG D 110 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 107 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT B 111 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC F 102 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT F 103 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG F 104 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA F 105 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DA F 105 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 102 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 107 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG C 111 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 10FY A 101 121 PDB 10FY 10FY 101 121 DBREF 10FY E 102 115 PDB 10FY 10FY 102 115 DBREF 10FY D 102 114 PDB 10FY 10FY 102 114 DBREF 10FY B 101 121 PDB 10FY 10FY 101 121 DBREF 10FY F 101 115 PDB 10FY 10FY 101 115 DBREF 10FY C 101 121 PDB 10FY 10FY 101 121 DBREF 10FY M 101 121 PDB 10FY 10FY 101 121 SEQRES 1 A 21 DC DC DG DA DT DG DC DC DT DG DA DT DC SEQRES 2 A 21 DG DG DA DC DA DA DG DA SEQRES 1 E 14 DT DA DG DT DC DG DT DG DG DC DA DT DC SEQRES 2 E 14 DG SEQRES 1 D 13 DG DT DC DT DT DG DT DG DG DT DC DG DC SEQRES 1 B 21 DG DA DG DC DG DA DC DC DT DG DT DA DC SEQRES 2 B 21 DG DG DA DC DA DT DC DA SEQRES 1 F 15 DT DC DT DG DA DT DG DT DG DG DT DA DG SEQRES 2 F 15 DG DT SEQRES 1 C 21 DA DA DC DC DT DA DC DC DT DG DG DC DA SEQRES 2 C 21 DG DG DA DC DG DA DC DT SEQRES 1 M 21 DA DC DA DC DC DG DA DT DC DA DC DC DT SEQRES 2 M 21 DG DC DC DA DC DC DG DT CRYST1 67.923 68.115 69.672 97.10 101.20 98.55 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 0.014723 0.002213 0.003304 0.00000 SCALE2 0.000000 0.014846 0.002363 0.00000 SCALE3 0.000000 0.000000 0.014816 0.00000 MASTER 238 0 0 0 0 0 0 6 2562 7 0 13 END