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Structure of human DNA polymerase beta complexed with 8-BrG as the template base in a 1-nucleotide gapped DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ISB PDB ENTRY 3ISB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 14-23% PEG 3340, 350mM sodium acetate in 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.554 α = 90 b = 79.271 β = 105.48 c = 54.915 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 100 IMAGE PLATE RIGAKU RAXIS IV++ 2013-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.27 20 97.1 20228 20228
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 3ISB 2.27 19.83 19695 1011 94.27 0.2151 0.212 0.2155 0.2694 0.2687 RANDOM 28.3099
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] 0.81 0.44 -0.49 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.116 r_dihedral_angle_3_deg 16.947 r_dihedral_angle_4_deg 16.637 r_dihedral_angle_1_deg 5.83 r_mcangle_it 2.731 r_mcbond_it 1.756 r_mcbond_other 1.745 r_angle_refined_deg 1.651 r_angle_other_deg 1.148 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.116 r_dihedral_angle_3_deg 16.947 r_dihedral_angle_4_deg 16.637 r_dihedral_angle_1_deg 5.83 r_mcangle_it 2.731 r_mcbond_it 1.756 r_mcbond_other 1.745 r_angle_refined_deg 1.651 r_angle_other_deg 1.148 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2543 Nucleic Acid Atoms 633 Solvent Atoms 72 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing