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Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HVI PDB entry 2HVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 290 50% Saturated ammonium sulfate, 0.1M MES, 2.5% v/v Methylpentanediol, 10mM Magnesium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.28 α = 90 b = 108.79 β = 90 c = 152.09 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97121 APS 22-BM
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 1.7 46.98 99.8 0.06 14.38 3.9 169954 169685 -3 26.76
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) 1 1.7 1.74 99.8 0.561 2.5 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2HVI 1.7 46.98 169685 169684 7528 100 0.2114 0.20974 0.2082 0.24686 0.2438 RANDOM 23.552
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 r_dihedral_angle_2_deg 33.114 r_dihedral_angle_4_deg 16.14 r_dihedral_angle_3_deg 14.151 r_dihedral_angle_1_deg 5.306 r_scangle_it 3.111 r_scbond_it 1.918 r_angle_refined_deg 1.325 r_mcangle_it 1.243 r_mcbond_it 0.653 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.114 r_dihedral_angle_4_deg 16.14 r_dihedral_angle_3_deg 14.151 r_dihedral_angle_1_deg 5.306 r_scangle_it 3.111 r_scbond_it 1.918 r_angle_refined_deg 1.325 r_mcangle_it 1.243 r_mcbond_it 0.653 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9292 Nucleic Acid Atoms 848 Solvent Atoms 996 Heterogen Atoms 170
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction REFMAC phasing