HEADER RNA 22-JUN-98 406D TITLE 5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(BRO) UP*CP*GP*GP*UP*G)-3' COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(5BU) COMPND 3 P*CP*GP*GP*UP*G)-3'); COMPND 4 CHAIN: A, E; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS DISORDERED, RNA, DOUBLE HELIX EXPDTA X-RAY DIFFRACTION NUMMDL 4 AUTHOR S.A.SHAH,A.T.BRUNGER REVDAT 4 28-FEB-24 406D 1 LINK ATOM REVDAT 3 16-NOV-11 406D 1 VERSN HETATM REVDAT 2 24-FEB-09 406D 1 VERSN REVDAT 1 05-FEB-99 406D 0 JRNL AUTH S.A.SHAH,A.T.BRUNGER JRNL TITL THE 1.8 A CRYSTAL STRUCTURE OF A STATICALLY DISORDERED 17 JRNL TITL 2 BASE-PAIR RNA DUPLEX: PRINCIPLES OF RNA CRYSTAL PACKING AND JRNL TITL 3 ITS EFFECT ON NUCLEIC ACID STRUCTURE. JRNL REF J.MOL.BIOL. V. 285 1577 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 9917398 JRNL DOI 10.1006/JMBI.1998.2385 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 382611.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 14484 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1524 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2079 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 227 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 726 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.43000 REMARK 3 B12 (A**2) : -0.53000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 10.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.420 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : CONSTR REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : DNA-RNA_REP.PA REMARK 3 PARAMETER FILE 2 : BR.PAR REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA_REP.PARAM REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED. THE STRUCTURE REMARK 3 OF STATICALLY DISORDERED 17-BP RNA DUPLEX IS REPRESENTED BY FOUR REMARK 3 MODELS IN THE ASYMMETRIC UNIT, EACH MODEL FOR A DISTINCT REMARK 3 CONFORMATION OF THE DUPLEX. THE SUM OF ALL MODELS CONTRIBUTE TO REMARK 3 THE OBSERVED DIFFRACTION DATA. TO GENERATE THE CONTENTS OF THE REMARK 3 ENTIRE ASYMMETRIC UNIT FROM THE FOUR DISORDERED DUPLEXES, A REMARK 3 STRICT NON-CRYSTALLOGRAPHIC HYPERSYMMETRY WAS APPLIED. REMARK 4 REMARK 4 406D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000179206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-95; NULL; NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 110.00; NULL; NULL; NULL REMARK 200 PH : 4.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; NULL; NULL; NULL REMARK 200 RADIATION SOURCE : NSLS; NULL; NULL; NULL REMARK 200 BEAMLINE : X12B; NULL; NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL; NULL; NULL REMARK 200 MONOCHROMATOR : NULL; NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; NULL; NULL; NULL REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; NULL; NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8052 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS 0.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE CRYSTAL PACKING OF 17-BP RNA DUPLEX IS STATICALLY REMARK 200 DISORDERED. AS A RESULT, THE ASYMMETRIC UNIT OF THE CRYSTAL REMARK 200 CONTAINS FOUR SUPERIMPOSED ORIENTATIONS OF THE DUPLEX THAT ARE REMARK 200 OUT OF REGISTER, SUCH THAT BACKBONES SUPERIMPOSE, BUT BASE REMARK 200 IDENTITY DIFFERS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.50, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.00K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -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 0.00000 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 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 APPLY THE FOLLOWING TO CHAINS: A, E 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 HOH A 18 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 19 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 30 LIES ON A SPECIAL POSITION. REMARK 375 HOH E 35 LIES ON A SPECIAL POSITION. REMARK 375 HOH E 36 LIES ON A SPECIAL POSITION. REMARK 375 HOH E 37 LIES ON A SPECIAL POSITION. REMARK 375 HOH E 38 LIES ON A SPECIAL POSITION. REMARK 375 HOH E 39 LIES ON A SPECIAL POSITION. REMARK 375 HOH E 41 LIES ON A SPECIAL POSITION. REMARK 375 HOH E 42 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THE CRYSTAL IS MADE OF STATICALLY DISORDERED 17-BP RNA DUPLEX. ALL REMARK 400 CONFIRMATIONS ARE REPRESENTED BY FOUR MODELS. DBREF 406D A 1 17 PDB 406D 406D 1 17 DBREF 406D E 18 34 PDB 406D 406D 18 34 SEQRES 1 A 17 C A C C G G A U G G U 5BU C SEQRES 2 A 17 G G U G SEQRES 1 E 17 C A C C G G A U G G U 5BU C SEQRES 2 E 17 G G U G MODRES 406D 5BU A 12 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 406D 5BU E 29 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE HET 5BU A 12 21 HET 5BU E 29 21 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE FORMUL 1 5BU 2(C9 H12 BR N2 O9 P) FORMUL 3 HOH *34(H2 O) LINK O3'A U A 11 P A5BU A 12 1555 1555 1.60 LINK O3'A5BU A 12 P A C A 13 1555 1555 1.61 LINK O3'A U E 28 P A5BU E 29 1555 1555 1.60 LINK O3'A5BU E 29 P A C E 30 1555 1555 1.60 CRYST1 39.627 39.627 91.018 90.00 90.00 120.00 P 3 6 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 0.025235 0.014570 0.000000 0.00000 SCALE2 0.000000 0.029139 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010987 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 2 0.000000 -1.000000 0.000000 68.64000 1 MTRIX3 2 0.000000 0.000000 -1.000000 182.03600 1 MODEL 1