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DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and 3'-amino primer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 1 M Malonic acid, 0.15 M Ammonium citrate tribasic, 0.07 M Succinic acid, 0.18 M DL-Malic acid, 0.24 M Sodium acetate trihydrate, 0.3 M Sodium formate, 0.1 M Ammonium tartrate dibasic, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.96 62.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.608 α = 90 b = 93.916 β = 90 c = 106.124 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 2.25 50 94.4 0.141 0.153 0.057 0.978 15.1 7 40025
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 2.25 2.33 83.2 0.574 0.628 0.245 0.802 6.8 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4DSI 2.25 28.4 1.35 40004 1946 94.43 0.2073 0.2054 0.2051 0.2442 0.2438 RANDOM
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 26.77 f_angle_d 1.818 f_chiral_restr 0.084 f_bond_d 0.013 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4649 Nucleic Acid Atoms 406 Solvent Atoms 164 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing