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DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 1 MONTH: PEG 1500, 15% HEPES, 75 MILLIMOLAR, PH 7.5 NACL, 50 MILLIMOLAR DTT, 0.1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.178 α = 90 b = 62.884 β = 90 c = 38.286 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 AREA DETECTOR XUONG-HAMLIN MULTIWIRE 1994-06-17 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 20 97 0.064 8.2 2.7 6027
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 92 0.166 1.9 1.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER 1BPB 3 20 6027 97 0.1701
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation t_dihedral_angle_d 22.6 t_it 5.8 t_angle_deg 2.7 t_nbd 0.023 t_bond_d 0.016 t_trig_c_planes 0.016 t_gen_planes 0.008 t_incorr_chiral_ct t_pseud_angle
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1928 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 1
Software Software Software Name Purpose TNT refinement SDMS data reduction SDMS data scaling TNT phasing