HEADER RNA 02-MAY-08 3D0M TITLE X-RAY STRUCTURES OF THE (GUGGUCUGAUGAGGCC) RNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)- COMPND 3 3'); COMPND 4 CHAIN: X; COMPND 5 FRAGMENT: DUPLEX FORMED BY THE SHORTER STRANDS OF HAMMERHEAD COMPND 6 RIBOZYME; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA, DUPLEX, BASE PAIRING, G(SYN) - G(ANTI), SULPHATE ANION EXPDTA X-RAY DIFFRACTION AUTHOR W.RYPNIEWSKI,D.A.ADAMIAK,J.MILECKI,R.W.ADAMIAK REVDAT 4 30-AUG-23 3D0M 1 REMARK REVDAT 3 25-OCT-17 3D0M 1 REMARK REVDAT 2 24-FEB-09 3D0M 1 VERSN REVDAT 1 09-SEP-08 3D0M 0 JRNL AUTH W.RYPNIEWSKI,D.A.ADAMIAK,J.MILECKI,R.W.ADAMIAK JRNL TITL NONCANONICAL G(SYN)-G(ANTI) BASE PAIRS STABILIZED BY JRNL TITL 2 SULPHATE ANIONS IN TWO X-RAY STRUCTURES OF THE JRNL TITL 3 (GUGGUCUGAUGAGGCC) RNA DUPLEX. JRNL REF RNA V. 14 1845 2008 JRNL REFN ISSN 1355-8382 JRNL PMID 18658118 JRNL DOI 10.1261/RNA.1164308 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 3372 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.295 REMARK 3 FREE R VALUE : 0.361 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.800 REMARK 3 FREE R VALUE TEST SET COUNT : 61 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 249 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4660 REMARK 3 BIN FREE R VALUE SET COUNT : 4 REMARK 3 BIN FREE R VALUE : 0.3790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 341 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.93000 REMARK 3 B22 (A**2) : 2.93000 REMARK 3 B33 (A**2) : -4.40000 REMARK 3 B12 (A**2) : 1.47000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.262 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.248 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.352 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.108 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 385 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 600 ; 3.978 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 79 ; 0.186 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 169 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 119 ; 0.231 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 222 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 9 ; 0.197 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 37 ; 0.239 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.166 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 560 ; 2.524 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 600 ; 4.149 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3D0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047441. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-04 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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8020 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3434 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 37.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.46300 REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: ANOTHER CRYSTAL FORM (PDB ID 3CZW) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULPHATE, 50 MM REMARK 280 CACODYLATE BUFFER, 15 MM MAGNESIUM ACETATE, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 23.32650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 13.46756 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 42.13233 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 23.32650 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 13.46756 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 42.13233 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 23.32650 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 13.46756 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 42.13233 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 23.32650 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 13.46756 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 42.13233 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 23.32650 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 13.46756 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 42.13233 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 23.32650 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 13.46756 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 42.13233 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 26.93512 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 84.26467 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 26.93512 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 84.26467 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 26.93512 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 84.26467 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 26.93512 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 84.26467 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 26.93512 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 84.26467 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 26.93512 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 84.26467 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: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 23.32650 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -13.46756 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 84.26467 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 S SO4 X 501 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 504 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 505 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 516 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 518 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 G X 1 O5' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G X 1 C2 G X 1 N3 0.054 REMARK 500 C X 6 C2' C X 6 C1' -0.074 REMARK 500 G X 13 C5 G X 13 N7 0.039 REMARK 500 G X 14 C5 G X 14 N7 0.037 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 G X 1 O4' - C4' - C3' ANGL. DEV. = -11.5 DEGREES REMARK 500 G X 1 C5' - C4' - O4' ANGL. DEV. = -12.4 DEGREES REMARK 500 G X 1 C4' - C3' - C2' ANGL. DEV. = 8.0 DEGREES REMARK 500 G X 1 C3' - C2' - C1' ANGL. DEV. = -8.5 DEGREES REMARK 500 G X 1 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES REMARK 500 G X 1 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 U X 2 O4' - C4' - C3' ANGL. DEV. = -10.0 DEGREES REMARK 500 U X 2 C1' - O4' - C4' ANGL. DEV. = 5.1 DEGREES REMARK 500 U X 2 C4' - C3' - C2' ANGL. DEV. = 6.1 DEGREES REMARK 500 U X 2 C3' - C2' - C1' ANGL. DEV. = -4.7 DEGREES REMARK 500 U X 2 C6 - N1 - C2 ANGL. DEV. = 3.8 DEGREES REMARK 500 U X 2 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 G X 3 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES REMARK 500 G X 3 C4' - C3' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 G X 3 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 G X 3 O4' - C1' - N9 ANGL. DEV. = -7.5 DEGREES REMARK 500 G X 4 N1 - C6 - O6 ANGL. DEV. = -4.4 DEGREES REMARK 500 G X 4 C5 - C6 - O6 ANGL. DEV. = 4.3 DEGREES REMARK 500 U X 5 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 U X 5 C4 - C5 - C6 ANGL. DEV. = -4.4 DEGREES REMARK 500 C X 6 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES REMARK 500 C X 6 C3' - C2' - C1' ANGL. DEV. = -7.8 DEGREES REMARK 500 C X 6 C6 - N1 - C2 ANGL. DEV. = 2.8 DEGREES REMARK 500 C X 6 N3 - C4 - C5 ANGL. DEV. = 3.4 DEGREES REMARK 500 C X 6 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 C X 6 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 U X 7 OP1 - P - OP2 ANGL. DEV. = 12.9 DEGREES REMARK 500 U X 7 O5' - P - OP1 ANGL. DEV. = -6.3 DEGREES REMARK 500 U X 7 P - O5' - C5' ANGL. DEV. = 12.9 DEGREES REMARK 500 U X 7 C3' - C2' - C1' ANGL. DEV. = -8.8 DEGREES REMARK 500 U X 7 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 U X 7 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 G X 8 P - O5' - C5' ANGL. DEV. = 11.8 DEGREES REMARK 500 G X 8 O4' - C4' - C3' ANGL. DEV. = -15.5 DEGREES REMARK 500 G X 8 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES REMARK 500 G X 8 C3' - C2' - C1' ANGL. DEV. = -8.1 DEGREES REMARK 500 G X 8 O4' - C1' - N9 ANGL. DEV. = 9.7 DEGREES REMARK 500 G X 8 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 A X 12 C3' - C2' - C1' ANGL. DEV. = -10.4 DEGREES REMARK 500 G X 13 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 G X 13 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES REMARK 500 G X 13 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES REMARK 500 G X 13 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 G X 13 C3' - O3' - P ANGL. DEV. = -7.3 DEGREES REMARK 500 G X 14 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 G X 14 C3' - C2' - C1' ANGL. DEV. = -7.1 DEGREES REMARK 500 G X 14 N3 - C4 - C5 ANGL. DEV. = 3.5 DEGREES REMARK 500 G X 14 C4 - C5 - C6 ANGL. DEV. = -5.5 DEGREES REMARK 500 G X 14 C4 - C5 - N7 ANGL. DEV. = 2.8 DEGREES REMARK 500 C X 15 O5' - C5' - C4' ANGL. DEV. = -5.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 54 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CZW RELATED DB: PDB REMARK 900 THE SAME MOLECULE IN DIFFERENT CRYSTAL FORM DBREF 3D0M X 1 16 PDB 3D0M 3D0M 1 16 SEQRES 1 X 16 G U G G U C U G A U G A G SEQRES 2 X 16 G C C HET SO4 X 501 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *19(H2 O) CRYST1 46.653 46.653 126.397 90.00 90.00 120.00 H 3 2 18 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 0.021435 0.012375 0.000000 0.00000 SCALE2 0.000000 0.024751 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007912 0.00000