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Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus Y714S mutant bound to G:T mismatch
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L3U PDB entry 1L3U
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 3.1 60.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.21 α = 90 b = 93.73 β = 90 c = 105.51 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 1.00000 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 1.74 45.98 90.6 0.084 10.66 5 92241 83554 -3 29.055
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 1.74 1.85 77.9 0.409 2.9 4.5 11929
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 PDB entry 1L3U 1.75 45.98 83554 4178 100 0.203 0.201 0.241 0.2499 RANDOM 25.3
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 32.559 r_dihedral_angle_4_deg 14.502 r_dihedral_angle_3_deg 13.839 r_dihedral_angle_1_deg 5.022 r_scangle_it 2.99 r_scbond_it 1.82 r_angle_refined_deg 1.17 r_mcangle_it 1.134 r_mcbond_it 0.584 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.559 r_dihedral_angle_4_deg 14.502 r_dihedral_angle_3_deg 13.839 r_dihedral_angle_1_deg 5.022 r_scangle_it 2.99 r_scbond_it 1.82 r_angle_refined_deg 1.17 r_mcangle_it 1.134 r_mcbond_it 0.584 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4649 Nucleic Acid Atoms 387 Solvent Atoms 724 Heterogen Atoms 58
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction PHASER phasing