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Bst DNA polymerase I Large Fragment wildtype D598A with 3'-amino primer, dGTP, and calcium time-resolved 48h (Product State)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2M ammonium sulphate, 0.1M MES pH 5.3-6.0, 20 mM CaCl2, 5% MPD
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.082 α = 90 b = 109.164 β = 90 c = 150.591 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 PIXEL DECTRIS EIGER X 16M 2021-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033175 APS 23-ID-B
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 2.38 50 98.7 0.107 0.121 0.054 0.988 11.8 4.7 61520 34.66
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 2.38 2.42 99.8 0.497 0.559 0.253 0.799 2.8 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.38 47.04 1.37 60654 3121 96.74 0.1896 0.1868 0.1872 0.2391 0.2393 42.06
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 f_dihedral_angle_d 23.5696 f_angle_d 0.9479 f_chiral_restr 0.0504 f_bond_d 0.0079 f_plane_restr 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9290 Nucleic Acid Atoms 900 Solvent Atoms 310 Heterogen Atoms 81
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing