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Structure of 9N-I DNA polymerase incorporation with dG in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Sodium Acetate pH4.6, MPD, Glycerol, CaCl2
Crystal Properties Matthews coefficient Solvent content 3.83 67.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.078 α = 90 b = 208.078 β = 90 c = 208.078 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD RAYONIX MX300-HS 2016-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
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 3.401 40.81 99.87 0.02677 0.999 8.35 2 20707
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 3.401 3.522 0.4758 0.585
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 4F8X 3.401 40.81 19647 1073 99.93 0.25472 0.25217 0.246 0.30168 0.292 RANDOM 129.153
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 r_dihedral_angle_2_deg 26.88 r_long_range_B_refined 18.636 r_long_range_B_other 18.636 r_dihedral_angle_3_deg 17.299 r_dihedral_angle_4_deg 9.923 r_dihedral_angle_1_deg 6.555 r_scangle_other 3.149 r_mcangle_it 2.403 r_mcangle_other 2.403 r_scbond_it 1.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.88 r_long_range_B_refined 18.636 r_long_range_B_other 18.636 r_dihedral_angle_3_deg 17.299 r_dihedral_angle_4_deg 9.923 r_dihedral_angle_1_deg 6.555 r_scangle_other 3.149 r_mcangle_it 2.403 r_mcangle_other 2.403 r_scbond_it 1.723 r_scbond_other 1.72 r_angle_other_deg 1.33 r_mcbond_it 1.318 r_mcbond_other 1.318 r_angle_refined_deg 1.29 r_chiral_restr 0.1 r_gen_planes_other 0.022 r_bond_refined_d 0.013 r_bond_other_d 0.011 r_gen_planes_refined 0.008 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 5245 Nucleic Acid Atoms 633 Solvent Atoms 51 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing