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Structure of human DNA polymerase beta complexed with 8OA 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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 14% TO 23% PEG3400, AND 350 MM SODIUM
ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING
DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.572 α = 90 b = 79.048 β = 105.75 c = 54.966 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++ 2014-05-12 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) 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 2.26 20 99.1 0.074 19.2 4 19876
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.32
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ISB 2.26 19.76 18787 1022 94.2 0.207 0.204 0.272 0.2375 RANDOM 36.4
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] -0.04 -0.46 -0.1 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.543 r_dihedral_angle_4_deg 18.482 r_dihedral_angle_3_deg 17.069 r_dihedral_angle_1_deg 6.477 r_angle_refined_deg 1.814 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.543 r_dihedral_angle_4_deg 18.482 r_dihedral_angle_3_deg 17.069 r_dihedral_angle_1_deg 6.477 r_angle_refined_deg 1.814 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2571 Nucleic Acid Atoms 632 Solvent Atoms 109 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction HKL-2000 data scaling MOLREP phasing PHASER phasing REFMAC refinement