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Structure of 9N-I DNA polymerase incorporation with dA in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K8X
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 3.15 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.951 α = 90 b = 106.767 β = 90 c = 255.903 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 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 2.8 46.29 99.41 0.04708 0.994 1.88 2 63508
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 0.335 0.703
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 4K8X 2.8 46.29 60118 3139 99.4 0.22748 0.22493 0.2248 0.27625 0.2706 RANDOM 81.663
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] -1.59 -2.78 4.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.961 r_dihedral_angle_3_deg 17.782 r_dihedral_angle_4_deg 16.153 r_dihedral_angle_1_deg 6.149 r_long_range_B_refined 4.628 r_long_range_B_other 4.628 r_mcangle_it 1.817 r_mcangle_other 1.817 r_scangle_other 1.749 r_angle_refined_deg 1.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.961 r_dihedral_angle_3_deg 17.782 r_dihedral_angle_4_deg 16.153 r_dihedral_angle_1_deg 6.149 r_long_range_B_refined 4.628 r_long_range_B_other 4.628 r_mcangle_it 1.817 r_mcangle_other 1.817 r_scangle_other 1.749 r_angle_refined_deg 1.225 r_angle_other_deg 1.151 r_mcbond_it 1.002 r_mcbond_other 1.002 r_scbond_it 0.961 r_scbond_other 0.961 r_chiral_restr 0.048 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 11606 Nucleic Acid Atoms 1564 Solvent Atoms 245 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing