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Structure of the family B DNA polymerase from the hyperthermophilic archaeon Pyrobaculum calidifontis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XHB 2xhb, 3a2f, 1wn7, 1s5j experimental model PDB 3A2F 2xhb, 3a2f, 1wn7, 1s5j experimental model PDB 1WN7 2xhb, 3a2f, 1wn7, 1s5j experimental model PDB 1S5J 2xhb, 3a2f, 1wn7, 1s5j
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 PEG 3350, potassium thiocyanate, Bis-Tris propane
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.19 α = 90 b = 100.742 β = 94.72 c = 119.335 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 118.93 97.5 0.1 0.99 6.8 3.6 42313
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 96.9 0.77 0.59 1.8 3.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2xhb, 3a2f, 1wn7, 1s5j 2.8 65.247 1.34 41959 2132 96.93 0.2537 0.2517 0.2536 0.2896 0.2923
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 10.925 f_angle_d 0.733 f_chiral_restr 0.048 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12260 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement MOLREP phasing Aimless data scaling DIALS data reduction