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Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with with natural dT:dATP base pair
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 293.15 0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.169 α = 90 b = 109.169 β = 90 c = 91.003 γ = 120
Symmetry Space Group P 31 2 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 2016-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9793 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.21 94.54 99.9 21.72 7.6 30234
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.25
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 4DFK 2.21 94.54 30234 1602 99.92 0.18713 0.18432 0.1915 0.23787 0.2361 RANDOM 49.112
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] 0.56 0.28 0.56 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 16.14 r_dihedral_angle_3_deg 15.942 r_dihedral_angle_1_deg 8.959 r_long_range_B_refined 3.19 r_long_range_B_other 3.19 r_angle_refined_deg 1.486 r_scangle_other 1.472 r_mcangle_it 1.224 r_mcangle_other 1.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 16.14 r_dihedral_angle_3_deg 15.942 r_dihedral_angle_1_deg 8.959 r_long_range_B_refined 3.19 r_long_range_B_other 3.19 r_angle_refined_deg 1.486 r_scangle_other 1.472 r_mcangle_it 1.224 r_mcangle_other 1.224 r_angle_other_deg 1.137 r_scbond_it 0.888 r_scbond_other 0.888 r_mcbond_it 0.747 r_mcbond_other 0.744 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4282 Nucleic Acid Atoms 568 Solvent Atoms 290 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing