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DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and primer containing an N3'-> P5' linkage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 10mM MgCl2, 0.8 M Succinic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.82 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.197 α = 90 b = 93.679 β = 90 c = 107.14 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 99 CCD MAR CCD 130 mm 2018-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 50 99.9 0.12 0.129 0.046 0.991 17.9 8 39951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.36 100 0.508 0.543 0.192 0.986 4.7 8
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 1L5U 2.27 40.85 37883 1970 99.08 0.2313 0.229 0.2323 0.2767 0.2777 RANDOM 42.616
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] 0.01 0.04 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.139 r_dihedral_angle_4_deg 20.265 r_dihedral_angle_3_deg 17.207 r_dihedral_angle_1_deg 6.967 r_angle_refined_deg 1.55 r_angle_other_deg 1.281 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.139 r_dihedral_angle_4_deg 20.265 r_dihedral_angle_3_deg 17.207 r_dihedral_angle_1_deg 6.967 r_angle_refined_deg 1.55 r_angle_other_deg 1.281 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4649 Nucleic Acid Atoms 449 Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing