HEADER DNA 04-AUG-22 8DYK TITLE ROOM TEMPERATURE NEUTRON STRUCTURE OF A FLUORESCENT AG8 CLUSTER TITLE 2 TEMPLATED BY A MULTISTRANDED DNA SCAFFOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*AP*CP*CP*CP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA, METAL CLUSTERS, SILVER, CHROMOPHORE EXPDTA NEUTRON DIFFRACTION AUTHOR F.MEILLEUR,R.L.LIEBERMAN,J.T.PETTY REVDAT 2 22-MAY-24 8DYK 1 REMARK REVDAT 1 02-AUG-23 8DYK 0 JRNL AUTH F.DAVID,C.SETZLER,A.SORESCU,R.L.LIEBERMAN,F.MEILLEUR, JRNL AUTH 2 J.T.PETTY JRNL TITL MAPPING H + IN THE NANOSCALE (A 2 C 4 ) 2 -AG 8 FLUOROPHORE. JRNL REF J PHYS CHEM LETT V. 13 11317 2022 JRNL REFN ESSN 1948-7185 JRNL PMID 36453924 JRNL DOI 10.1021/ACS.JPCLETT.2C03161 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.650 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 2315 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.110 REMARK 3 FREE R VALUE TEST SET COUNT : 232 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 12.2600 - 2.6400 0.97 1079 122 0.1888 0.2403 REMARK 3 2 2.6400 - 2.1000 0.97 1002 112 0.2902 0.3701 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) : 0.374 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.925 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.74 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 : 0.006 426 REMARK 3 ANGLE : 0.795 717 REMARK 3 CHIRALITY : 0.038 46 REMARK 3 PLANARITY : 0.002 20 REMARK 3 DIHEDRAL : 25.699 127 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 8DYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267558. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 07-MAY-21 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 6.00 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : SPALLATION SOURCE REMARK 230 BEAMLINE : MANDI REMARK 230 WAVELENGTH OR RANGE (A) : 2.0-4.0 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : AREA DETECTOR REMARK 230 DETECTOR MANUFACTURER : ORNL ANGER CAMERA REMARK 230 INTENSITY-INTEGRATION SOFTWARE : MANTID REMARK 230 DATA SCALING SOFTWARE : LAUENORM REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 2315 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 230 RESOLUTION RANGE LOW (A) : 12.260 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 230 DATA REDUNDANCY : 6.200 REMARK 230 R MERGE (I) : 0.14600 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 10.5000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 230 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 230 DATA REDUNDANCY IN SHELL : 5.60 REMARK 230 R MERGE FOR SHELL (I) : 0.26350 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 3.770 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : PHASER REMARK 230 STARTING MODEL: 6NIZ REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 MM A2C4, 9MM AGNO3, 70 MM REMARK 280 CACODYLATE BUFFER (PH 6), 2-METHYL-2,4-PENTANEDIOL (MPD), VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 31.87050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 16.78400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 16.78400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.93525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 16.78400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 16.78400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.80575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 16.78400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 16.78400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.93525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 16.78400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 16.78400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.80575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 31.87050 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: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 AG AG A 107 LIES ON A SPECIAL POSITION. 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 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES 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 AG A 105 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 1 N1 REMARK 620 2 HOH A 205 O 113.3 REMARK 620 3 DA B 1 N6 101.4 126.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 104 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 2 N7 REMARK 620 2 HOH A 213 O 140.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 106 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 2 N1 REMARK 620 2 HOH A 206 O 91.1 REMARK 620 3 DA B 1 N1 100.4 16.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 107 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 2 N3 REMARK 620 2 DA A 2 N3 0.0 REMARK 620 3 HOH A 215 O 114.2 114.2 REMARK 620 4 HOH A 215 O 123.8 123.8 10.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG B 102 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 2 N6 REMARK 620 2 DA B 2 N1 168.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 103 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 3 O2 REMARK 620 2 DC A 3 N3 53.1 REMARK 620 3 DA B 2 N6 151.6 155.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG B 101 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 3 N4 REMARK 620 2 DC B 3 N3 150.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 102 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 4 N3 REMARK 620 2 DC B 4 O2 142.8 REMARK 620 3 DC B 4 N3 161.1 54.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 108 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 4 OP1 REMARK 620 2 DC A 6 N3 10.8 REMARK 620 3 DC B 6 N3 19.3 14.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 101 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 5 N3 REMARK 620 2 DC B 5 N3 160.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG B 103 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA B 1 N3 REMARK 620 2 DA B 1 N3 0.0 REMARK 620 3 DA B 2 N7 97.5 97.5 REMARK 620 4 DA B 2 N7 97.5 97.5 0.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6NIZ RELATED DB: PDB DBREF 8DYK A 1 6 PDB 8DYK 8DYK 1 6 DBREF 8DYK B 1 6 PDB 8DYK 8DYK 1 6 SEQRES 1 A 6 DA DA DC DC DC DC SEQRES 1 B 6 DA DA DC DC DC DC HET AG A 101 1 HET AG A 102 1 HET AG A 103 1 HET AG A 104 1 HET AG A 105 1 HET AG A 106 1 HET AG A 107 1 HET AG A 108 1 HET AG B 101 1 HET AG B 102 1 HET AG B 103 1 HETNAM AG SILVER ION FORMUL 3 AG 11(AG 1+) FORMUL 14 HOH *24(H2 O) LINK N1 DA A 1 AG AG A 105 1555 1555 2.22 LINK N7 DA A 2 AG AG A 104 1555 1555 2.42 LINK N1 DA A 2 AG AG A 106 1555 1555 2.37 LINK N3 DA A 2 AG AG A 107 1555 1555 2.52 LINK N3 DA A 2 AG AG A 107 1555 8555 2.36 LINK N6 DA A 2 AG AG B 102 1555 1555 2.11 LINK O2 DC A 3 AG AG A 103 1555 1555 2.70 LINK N3 DC A 3 AG AG A 103 1555 1555 2.31 LINK N4 DC A 3 AG AG B 101 1555 1555 2.23 LINK N3 DC A 4 AG AG A 102 1555 1555 2.15 LINK OP1 DC A 4 AG AG A 108 1555 6455 2.64 LINK N3 DC A 5 AG AG A 101 1555 1555 2.22 LINK N3 DC A 6 AG AG A 108 1555 1555 2.30 LINK AG AG A 101 N3 DC B 5 1555 1555 2.16 LINK AG AG A 102 O2 DC B 4 1555 1555 2.63 LINK AG AG A 102 N3 DC B 4 1555 1555 2.22 LINK AG AG A 103 N6 DA B 2 1555 1555 2.06 LINK AG AG A 104 O HOH A 213 1555 1555 2.16 LINK AG AG A 105 O HOH A 205 1555 1555 2.45 LINK AG AG A 105 N6 DA B 1 8555 1555 2.34 LINK AG AG A 106 O HOH A 206 1555 8555 2.55 LINK AG AG A 106 N1 DA B 1 8555 1555 2.16 LINK AG AG A 107 O HOH A 215 1555 1555 2.33 LINK AG AG A 107 O HOH A 215 1555 8555 2.31 LINK AG AG A 108 N3 DC B 6 1555 1555 2.21 LINK N3 DA B 1 AG AG B 103 1555 1555 2.30 LINK N3 DA B 1 AG AG B 103 1555 8555 2.46 LINK N1 DA B 2 AG AG B 102 1555 1555 2.14 LINK N7 DA B 2 AG AG B 103 1555 1555 2.66 LINK N7 DA B 2 AG AG B 103 1555 8555 2.35 LINK N3 DC B 3 AG AG B 101 1555 1555 2.22 CRYST1 33.568 33.568 63.741 90.00 90.00 90.00 P 41 21 2 16 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 0.029790 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015688 0.00000