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HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE ADENINE AND INCOMING CYTIDINE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BPY PDB ENTRY 1BPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 290 14% PEG 3350, 350mM sodium Acetate, 50mM imidazole, 10mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.38 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.68 α = 90 b = 79.65 β = 106.77 c = 54.67 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 IMAGE PLATE RIGAKU RAXIS IV YALE MIRRORS 1998-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2 52.4 0.186 23.4 3.4 29484 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 75.1 0.186 4.38 2.26
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BPY 2 50 29439 1424 96.7 0.179 0.179 0.18 0.239 0.2375 RANDOM 27.36
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] 1.255 1.939 0.696 -1.951
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_scangle_it 4.64 c_scbond_it 3.297 c_mcangle_it 2.836 c_angle_deg 2.7 c_mcbond_it 2.091 c_improper_angle_d 1.11 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_scangle_it 4.64 c_scbond_it 3.297 c_mcangle_it 2.836 c_angle_deg 2.7 c_mcbond_it 2.091 c_improper_angle_d 1.11 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2703 Nucleic Acid Atoms 650 Solvent Atoms 790 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing