HEADER RNA 12-AUG-20 7JRT TITLE CRYSTAL STRUCTURES OF ARTIFICIALLY DESIGNED HOMOMERIC RNA TITLE 2 NANOARCHITECTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA NANO BRACELET; 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 NANO STRUCTURE, DIMERIC PARALLELOGRAM, RNA EXPDTA X-RAY DIFFRACTION AUTHOR D.LIU,Y.SHAO,J.A.PICCIRILLI,Y.WEIZMANN REVDAT 3 18-OCT-23 7JRT 1 REMARK REVDAT 2 06-OCT-21 7JRT 1 JRNL REVDAT 1 08-SEP-21 7JRT 0 JRNL AUTH D.LIU,Y.SHAO,J.A.PICCIRILLI,Y.WEIZMANN JRNL TITL STRUCTURES OF ARTIFICIALLY DESIGNED DISCRETE RNA JRNL TITL 2 NANOARCHITECTURES AT NEAR-ATOMIC RESOLUTION. JRNL REF SCI ADV V. 7 F4459 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 34550747 JRNL DOI 10.1126/SCIADV.ABF4459 REMARK 2 REMARK 2 RESOLUTION. 3.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 18129 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1758 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 45.5300 - 7.2098 0.99 1318 132 0.1636 0.1810 REMARK 3 2 7.2098 - 5.7262 0.99 1287 135 0.1936 0.2151 REMARK 3 3 5.7262 - 5.0034 1.00 1268 149 0.1786 0.2307 REMARK 3 4 5.0034 - 4.5464 0.99 1259 134 0.2013 0.2638 REMARK 3 5 4.5464 - 4.2208 0.99 1282 129 0.1958 0.2183 REMARK 3 6 4.2208 - 3.9721 0.99 1251 137 0.1836 0.2270 REMARK 3 7 3.9721 - 3.7733 0.99 1263 138 0.1795 0.2064 REMARK 3 8 3.7733 - 3.6091 0.99 1248 145 0.1967 0.2625 REMARK 3 9 3.6091 - 3.4702 0.97 1250 129 0.2055 0.2755 REMARK 3 10 3.4702 - 3.3505 0.98 1238 146 0.2194 0.2878 REMARK 3 11 3.3505 - 3.2457 0.98 1237 135 0.2101 0.2467 REMARK 3 12 3.2457 - 3.1530 0.98 1237 123 0.2158 0.2754 REMARK 3 13 3.1530 - 3.0700 0.96 1233 126 0.2409 0.2878 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.65 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 6408 REMARK 3 ANGLE : 1.220 9988 REMARK 3 CHIRALITY : 0.073 1340 REMARK 3 PLANARITY : 0.006 268 REMARK 3 DIHEDRAL : 15.029 3210 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 7JRT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10480 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 718 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 718 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18129 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.070 REMARK 200 RESOLUTION RANGE LOW (A) : 45.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 16.20 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51000 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: PHENIX 1.10.1_2155 REMARK 200 STARTING MODEL: PDB ID: 2NOK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80 MM NACL, 12 MM KCL, 20 MM MGCL2, 40 REMARK 280 MM SODIUM CACODYLATE PH 6.0, 30 % (V/V) MPD, 12 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 35.99500 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 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 N4 C A 8 O6 G A 60 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 C A 8 N3 - C4 - C5 ANGL. DEV. = 3.0 DEGREES REMARK 500 G A 15 C4 - C5 - N7 ANGL. DEV. = -2.4 DEGREES REMARK 500 A A 26 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 C A 27 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 C A 27 N1 - C2 - O2 ANGL. DEV. = 7.8 DEGREES REMARK 500 C A 27 N3 - C4 - N4 ANGL. DEV. = 4.6 DEGREES REMARK 500 C A 27 C5 - C4 - N4 ANGL. DEV. = -5.7 DEGREES REMARK 500 C A 27 C6 - N1 - C1' ANGL. DEV. = -11.2 DEGREES REMARK 500 C A 27 C2 - N1 - C1' ANGL. DEV. = 11.8 DEGREES REMARK 500 A A 37 O3' - P - OP2 ANGL. DEV. = -22.5 DEGREES REMARK 500 A A 37 O3' - P - OP1 ANGL. DEV. = -21.4 DEGREES REMARK 500 A A 37 OP1 - P - OP2 ANGL. DEV. = 12.3 DEGREES REMARK 500 G A 50 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 G A 50 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 G A 50 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 50 N1 - C6 - O6 ANGL. DEV. = -4.4 DEGREES REMARK 500 G A 50 C5 - C6 - O6 ANGL. DEV. = 3.7 DEGREES REMARK 500 C A 94 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 105 O3' - P - OP2 ANGL. DEV. = 9.4 DEGREES REMARK 500 C B 8 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 C B 27 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 A B 103 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 G B 105 N3 - C4 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 G B 105 C8 - N9 - C1' ANGL. DEV. = -8.1 DEGREES REMARK 500 G B 105 C4 - N9 - C1' ANGL. DEV. = 9.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 7JRT A 1 134 PDB 7JRT 7JRT 1 134 DBREF 7JRT B 1 134 PDB 7JRT 7JRT 1 134 SEQRES 1 A 134 G G A U A U U C G A C G G SEQRES 2 A 134 A G G C A C C C A G G A A SEQRES 3 A 134 C U A C C G U U G A A G C SEQRES 4 A 134 U C G C A C G A C G G C C SEQRES 5 A 134 U G G G G U C G A G U A U SEQRES 6 A 134 C C C G G U A U U U G U C SEQRES 7 A 134 G C G A G C A C U G A G G SEQRES 8 A 134 A A C U A C U G C U G A A SEQRES 9 A 134 G C C U C C A C G G C A G SEQRES 10 A 134 C C U C A G G A C A A G U SEQRES 11 A 134 A C C G SEQRES 1 B 134 G G A U A U U C G A C G G SEQRES 2 B 134 A G G C A C C C A G G A A SEQRES 3 B 134 C U A C C G U U G A A G C SEQRES 4 B 134 U C G C A C G A C G G C C SEQRES 5 B 134 U G G G G U C G A G U A U SEQRES 6 B 134 C C C G G U A U U U G U C SEQRES 7 B 134 G C G A G C A C U G A G G SEQRES 8 B 134 A A C U A C U G C U G A A SEQRES 9 B 134 G C C U C C A C G G C A G SEQRES 10 B 134 C C U C A G G A C A A G U SEQRES 11 B 134 A C C G CRYST1 86.436 71.990 89.439 90.00 117.61 90.00 P 1 21 1 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 0.011569 0.000000 0.006051 0.00000 SCALE2 0.000000 0.013891 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012618 0.00000