HEADER RNA 06-OCT-10 3P4B TITLE ALTERNATINGLY MODIFIED 2'FLUORO RNA OCTAMER F/RA2U2-P3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED MODIFIED RNA OCTAMER KEYWDS RNA, 2'-FLUORO-RNA, O2'-MODIFICATION, OCTAMER, 2'-FLUORO 2'- KEYWDS 2 DEOXYCYTIDINE, 2'-FLUORO 2'-DEOXYADENOSINE, 2'-FLUORO 2'- KEYWDS 3 DEOXYURIDINE, SIRNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,E.M.GREENE,P.A.JICMAN,R.K.PANDEY,M.MANOHARAN,E.ROZNERS, AUTHOR 2 M.EGLI REVDAT 3 06-SEP-23 3P4B 1 REMARK LINK REVDAT 2 11-MAY-11 3P4B 1 JRNL REVDAT 1 05-JAN-11 3P4B 0 JRNL AUTH P.S.PALLAN,E.M.GREENE,P.A.JICMAN,R.K.PANDEY,M.MANOHARAN, JRNL AUTH 2 E.ROZNERS,M.EGLI JRNL TITL UNEXPECTED ORIGINS OF THE ENHANCED PAIRING AFFINITY OF JRNL TITL 2 2'-FLUORO-MODIFIED RNA. JRNL REF NUCLEIC ACIDS RES. V. 39 3482 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21183463 JRNL DOI 10.1093/NAR/GKQ1270 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21294 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1141 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1343 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1002 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.80000 REMARK 3 B22 (A**2) : 0.80000 REMARK 3 B33 (A**2) : -1.20000 REMARK 3 B12 (A**2) : 0.40000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.288 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1096 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1692 ; 2.077 ; 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): 226 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 490 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1096 ; 4.153 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1692 ; 4.966 ; 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): 1096 ; 3.503 ; 3.000 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 101 X 108 REMARK 3 RESIDUE RANGE : A 201 X 208 REMARK 3 ORIGIN FOR THE GROUP (A): -0.6160 14.0012 0.5898 REMARK 3 T TENSOR REMARK 3 T11: 0.0513 T22: 0.0441 REMARK 3 T33: 0.0491 T12: 0.0074 REMARK 3 T13: -0.0242 T23: -0.0371 REMARK 3 L TENSOR REMARK 3 L11: 1.0840 L22: 3.1172 REMARK 3 L33: 0.8509 L12: 0.0666 REMARK 3 L13: -1.0359 L23: -0.5205 REMARK 3 S TENSOR REMARK 3 S11: 0.0145 S12: 0.0404 S13: -0.1650 REMARK 3 S21: -0.2232 S22: 0.0367 S23: 0.1827 REMARK 3 S31: 0.0569 S32: 0.0611 S33: -0.0512 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 301 X 308 REMARK 3 RESIDUE RANGE : A 401 X 408 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8417 10.9764 -21.0515 REMARK 3 T TENSOR REMARK 3 T11: 0.0474 T22: 0.0444 REMARK 3 T33: 0.0551 T12: -0.0058 REMARK 3 T13: 0.0272 T23: -0.0430 REMARK 3 L TENSOR REMARK 3 L11: 1.2227 L22: 3.3141 REMARK 3 L33: 1.2268 L12: -0.0957 REMARK 3 L13: 1.1926 L23: -0.5788 REMARK 3 S TENSOR REMARK 3 S11: 0.0193 S12: -0.0529 S13: 0.1928 REMARK 3 S21: 0.2360 S22: 0.0567 S23: 0.2027 REMARK 3 S31: -0.0614 S32: 0.0911 S33: -0.0760 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 501 X 508 REMARK 3 RESIDUE RANGE : A 601 X 608 REMARK 3 ORIGIN FOR THE GROUP (A): 7.9514 12.5463 20.3729 REMARK 3 T TENSOR REMARK 3 T11: 0.0531 T22: 0.0238 REMARK 3 T33: 0.0656 T12: 0.0011 REMARK 3 T13: 0.0011 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.9392 L22: 3.3597 REMARK 3 L33: 0.1700 L12: -0.0895 REMARK 3 L13: -0.0623 L23: 1.3100 REMARK 3 S TENSOR REMARK 3 S11: 0.2481 S12: 0.0061 S13: 0.0039 REMARK 3 S21: 0.0106 S22: -0.1537 S23: -0.2427 REMARK 3 S31: -0.0041 S32: -0.1091 S33: -0.0944 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3P4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21294 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.340 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 3P4A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE (40 MM, PH 6.0), REMARK 280 SODIUM CHLORIDE (80 MM), BARIUM CHLORIDE (20 MM), SPERMINE REMARK 280 TETRAHYDROCHLORIDE (12 MM), AND 2-METHYL-2,4-PENTANEDIOL (MPD; REMARK 280 10% (V/V)), EQUILIBRATED AGAINST A RESERVOIR OF MPD (1 ML, 35%), REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 803 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 769 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 822 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 743 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 744 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 U E 506 C5' C4' O4' C3' C2' O2' C1' REMARK 480 U F 606 C5' C4' O4' C3' C2' O2' C1' 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 O HOH D 731 O HOH D 798 2.19 REMARK 500 O HOH A 721 O HOH A 830 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 A B 204 C2 A B 204 N3 0.054 REMARK 500 A B 204 N7 A B 204 C8 0.056 REMARK 500 U B 206 C2' U B 206 C1' -0.068 REMARK 500 G B 208 N7 G B 208 C8 0.042 REMARK 500 A C 304 C2 A C 304 N3 0.071 REMARK 500 A C 304 N7 A C 304 C8 0.066 REMARK 500 U C 306 C2' U C 306 C1' -0.073 REMARK 500 G D 402 C6 G D 402 N1 0.045 REMARK 500 G E 502 C6 G E 502 O6 -0.060 REMARK 500 U E 506 O5' U E 506 C5' -0.111 REMARK 500 G E 508 N7 G E 508 C8 0.038 REMARK 500 U F 606 O5' U F 606 C5' -0.324 REMARK 500 U F 606 O3' U F 606 C3' 0.134 REMARK 500 G F 608 N7 G F 608 C8 0.056 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 U E 506 P - O5' - C5' ANGL. DEV. = 12.0 DEGREES REMARK 500 U E 506 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 U E 506 C3' - O3' - P ANGL. DEV. = 14.4 DEGREES REMARK 500 U F 606 P - O5' - C5' ANGL. DEV. = 11.1 DEGREES REMARK 500 U F 606 C2 - N1 - C1' ANGL. DEV. = -7.3 DEGREES REMARK 500 U F 606 C3' - O3' - P ANGL. DEV. = -10.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 U E 506 0.06 SIDE CHAIN REMARK 500 U F 606 0.06 SIDE CHAIN 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 BA A 701 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UFT A 105 O4 REMARK 620 2 HOH A 729 O 72.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA D 702 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UFT D 405 O4 REMARK 620 2 HOH D 734 O 71.2 REMARK 620 3 HOH D 825 O 80.0 59.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA D 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3P4C RELATED DB: PDB REMARK 900 RELATED ID: 3P4D RELATED DB: PDB DBREF 3P4B A 101 108 PDB 3P4B 3P4B 101 108 DBREF 3P4B B 201 208 PDB 3P4B 3P4B 201 208 DBREF 3P4B C 301 308 PDB 3P4B 3P4B 301 308 DBREF 3P4B D 401 408 PDB 3P4B 3P4B 401 408 DBREF 3P4B E 501 508 PDB 3P4B 3P4B 501 508 DBREF 3P4B F 601 608 PDB 3P4B 3P4B 601 608 SEQRES 1 A 8 CFZ G AF2 A UFT U CFZ G SEQRES 1 B 8 CFZ G AF2 A UFT U CFZ G SEQRES 1 C 8 CFZ G AF2 A UFT U CFZ G SEQRES 1 D 8 CFZ G AF2 A UFT U CFZ G SEQRES 1 E 8 CFZ G AF2 A UFT U CFZ G SEQRES 1 F 8 CFZ G AF2 A UFT U CFZ G MODRES 3P4B CFZ A 101 DC MODRES 3P4B AF2 A 103 DA MODRES 3P4B UFT A 105 DU MODRES 3P4B CFZ A 107 DC MODRES 3P4B CFZ B 201 DC MODRES 3P4B AF2 B 203 DA MODRES 3P4B UFT B 205 DU MODRES 3P4B CFZ B 207 DC MODRES 3P4B CFZ C 301 DC MODRES 3P4B AF2 C 303 DA MODRES 3P4B UFT C 305 DU MODRES 3P4B CFZ C 307 DC MODRES 3P4B CFZ D 401 DC MODRES 3P4B AF2 D 403 DA MODRES 3P4B UFT D 405 DU MODRES 3P4B CFZ D 407 DC MODRES 3P4B CFZ E 501 DC MODRES 3P4B AF2 E 503 DA MODRES 3P4B UFT E 505 DU MODRES 3P4B CFZ E 507 DC MODRES 3P4B CFZ F 601 DC MODRES 3P4B AF2 F 603 DA MODRES 3P4B UFT F 605 DU MODRES 3P4B CFZ F 607 DC HET CFZ A 101 17 HET AF2 A 103 22 HET UFT A 105 20 HET CFZ A 107 20 HET CFZ B 201 17 HET AF2 B 203 22 HET UFT B 205 20 HET CFZ B 207 20 HET CFZ C 301 17 HET AF2 C 303 22 HET UFT C 305 20 HET CFZ C 307 20 HET CFZ D 401 17 HET AF2 D 403 22 HET UFT D 405 20 HET CFZ D 407 20 HET CFZ E 501 17 HET AF2 E 503 22 HET UFT E 505 20 HET CFZ E 507 20 HET CFZ F 601 17 HET AF2 F 603 22 HET UFT F 605 20 HET CFZ F 607 20 HET BA A 701 1 HET BA D 702 1 HETNAM CFZ 2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM AF2 2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM UFT 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM BA BARIUM ION FORMUL 1 CFZ 12(C9 H13 F N3 O7 P) FORMUL 1 AF2 6(C10 H13 F N5 O6 P) FORMUL 1 UFT 6(C9 H12 F N2 O8 P) FORMUL 7 BA 2(BA 2+) FORMUL 9 HOH *141(H2 O) LINK O3' CFZ A 101 P G A 102 1555 1555 1.61 LINK O3' G A 102 P AF2 A 103 1555 1555 1.62 LINK O3' AF2 A 103 P A A 104 1555 1555 1.62 LINK O3' A A 104 P UFT A 105 1555 1555 1.64 LINK O3' UFT A 105 P U A 106 1555 1555 1.62 LINK O3' U A 106 P CFZ A 107 1555 1555 1.63 LINK O3' CFZ A 107 P G A 108 1555 1555 1.62 LINK O3' CFZ B 201 P G B 202 1555 1555 1.58 LINK O3' G B 202 P AF2 B 203 1555 1555 1.59 LINK O3' AF2 B 203 P A B 204 1555 1555 1.61 LINK O3' A B 204 P UFT B 205 1555 1555 1.60 LINK O3' UFT B 205 P U B 206 1555 1555 1.62 LINK O3' U B 206 P CFZ B 207 1555 1555 1.58 LINK O3' CFZ B 207 P G B 208 1555 1555 1.56 LINK O3' CFZ C 301 P G C 302 1555 1555 1.56 LINK O3' G C 302 P AF2 C 303 1555 1555 1.58 LINK O3' AF2 C 303 P A C 304 1555 1555 1.62 LINK O3' A C 304 P UFT C 305 1555 1555 1.58 LINK O3' UFT C 305 P U C 306 1555 1555 1.65 LINK O3' U C 306 P CFZ C 307 1555 1555 1.59 LINK O3' CFZ C 307 P G C 308 1555 1555 1.55 LINK O3' CFZ D 401 P G D 402 1555 1555 1.62 LINK O3' G D 402 P AF2 D 403 1555 1555 1.60 LINK O3' AF2 D 403 P A D 404 1555 1555 1.63 LINK O3' A D 404 P UFT D 405 1555 1555 1.62 LINK O3' UFT D 405 P U D 406 1555 1555 1.61 LINK O3' U D 406 P CFZ D 407 1555 1555 1.63 LINK O3' CFZ D 407 P G D 408 1555 1555 1.62 LINK O3' CFZ E 501 P G E 502 1555 1555 1.60 LINK O3' G E 502 P AF2 E 503 1555 1555 1.62 LINK O3' AF2 E 503 P A E 504 1555 1555 1.63 LINK O3' A E 504 P UFT E 505 1555 1555 1.63 LINK O3' UFT E 505 P U E 506 1555 1555 1.61 LINK O3' U E 506 P CFZ E 507 1555 1555 1.60 LINK O3' CFZ E 507 P G E 508 1555 1555 1.65 LINK O3' CFZ F 601 P G F 602 1555 1555 1.58 LINK O3' G F 602 P AF2 F 603 1555 1555 1.62 LINK O3' AF2 F 603 P A F 604 1555 1555 1.61 LINK O3' A F 604 P UFT F 605 1555 1555 1.64 LINK O3' UFT F 605 P U F 606 1555 1555 1.59 LINK O3' U F 606 P CFZ F 607 1555 1555 1.61 LINK O3' CFZ F 607 P G F 608 1555 1555 1.60 LINK O4 UFT A 105 BA BA A 701 1555 1555 3.00 LINK BA BA A 701 O HOH A 729 1555 1555 2.80 LINK O4 UFT D 405 BA BA D 702 1555 1555 3.01 LINK BA BA D 702 O HOH D 734 1555 1555 2.77 LINK BA BA D 702 O HOH D 825 1555 1555 2.52 SITE 1 AC1 3 UFT A 105 HOH A 729 HOH A 775 SITE 1 AC2 3 UFT D 405 HOH D 734 HOH D 825 CRYST1 43.383 43.383 60.987 90.00 90.00 120.00 P 3 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 0.023051 0.013308 0.000000 0.00000 SCALE2 0.000000 0.026616 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016397 0.00000 HETATM 1 N1 CFZ A 101 4.355 6.801 7.334 1.00 15.37 N ANISOU 1 N1 CFZ A 101 1767 2347 1723 -159 405 265 N HETATM 2 C2 CFZ A 101 3.078 6.884 7.995 1.00 13.70 C ANISOU 2 C2 CFZ A 101 1504 1984 1717 119 186 763 C HETATM 3 O2 CFZ A 101 2.425 5.870 8.116 1.00 15.01 O ANISOU 3 O2 CFZ A 101 1556 1879 2266 -25 -43 474 O HETATM 4 N3 CFZ A 101 2.623 8.079 8.438 1.00 12.51 N ANISOU 4 N3 CFZ A 101 1503 1659 1589 35 177 538 N HETATM 5 C4 CFZ A 101 3.359 9.190 8.283 1.00 14.22 C ANISOU 5 C4 CFZ A 101 1551 1837 2013 -22 293 560 C HETATM 6 N4 CFZ A 101 2.886 10.362 8.726 1.00 17.76 N ANISOU 6 N4 CFZ A 101 1634 2668 2443 -195 412 275 N HETATM 7 C5 CFZ A 101 4.665 9.130 7.622 1.00 17.29 C ANISOU 7 C5 CFZ A 101 1548 2892 2128 -125 415 147 C HETATM 8 C6 CFZ A 101 5.109 7.951 7.188 1.00 19.69 C ANISOU 8 C6 CFZ A 101 2414 2796 2269 -249 40 450 C HETATM 9 C1' CFZ A 101 4.830 5.481 6.890 1.00 17.80 C ANISOU 9 C1' CFZ A 101 1955 2754 2054 -127 311 465 C HETATM 10 C2' CFZ A 101 4.126 4.899 5.685 1.00 14.67 C ANISOU 10 C2' CFZ A 101 1876 2128 1568 -277 419 375 C HETATM 11 F2' CFZ A 101 4.147 3.532 5.799 1.00 18.48 F ANISOU 11 F2' CFZ A 101 2139 2881 2001 307 762 640 F HETATM 12 C3' CFZ A 101 5.081 5.367 4.565 1.00 19.67 C ANISOU 12 C3' CFZ A 101 2042 3377 2052 24 342 387 C HETATM 13 O3' CFZ A 101 4.935 4.601 3.383 1.00 19.00 O ANISOU 13 O3' CFZ A 101 1934 3121 2163 519 34 469 O HETATM 14 C4' CFZ A 101 6.400 5.039 5.215 1.00 21.00 C ANISOU 14 C4' CFZ A 101 2298 3356 2325 209 181 298 C HETATM 15 O4' CFZ A 101 6.207 5.531 6.585 1.00 19.01 O ANISOU 15 O4' CFZ A 101 2037 3213 1970 -105 217 695 O HETATM 16 C5' CFZ A 101 7.557 5.750 4.601 1.00 20.84 C ANISOU 16 C5' CFZ A 101 2149 2967 2802 348 493 409 C HETATM 17 O5' CFZ A 101 7.412 7.117 4.706 1.00 23.01 O ANISOU 17 O5' CFZ A 101 2270 3067 3403 -145 842 690 O