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Structure of 9N-I DNA polymerase incorporation with 3'-CL 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 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.204 α = 90 b = 205.204 β = 90 c = 205.204 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 2017-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 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 3.2 40.24 99.85 0.024 0.99 9.12 2 23807
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 3.2 3.314 0.41 0.71
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 3.2 40.24 22579 1243 99.92 0.23492 0.23188 0.2305 0.29019 0.2838 RANDOM 106.389
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 28.87 r_dihedral_angle_3_deg 18.122 r_dihedral_angle_4_deg 14.519 r_long_range_B_refined 6.789 r_long_range_B_other 6.789 r_dihedral_angle_1_deg 6.599 r_scangle_other 3.322 r_mcangle_it 2.471 r_mcangle_other 2.471 r_scbond_it 1.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.87 r_dihedral_angle_3_deg 18.122 r_dihedral_angle_4_deg 14.519 r_long_range_B_refined 6.789 r_long_range_B_other 6.789 r_dihedral_angle_1_deg 6.599 r_scangle_other 3.322 r_mcangle_it 2.471 r_mcangle_other 2.471 r_scbond_it 1.932 r_scbond_other 1.932 r_mcbond_it 1.374 r_mcbond_other 1.374 r_angle_refined_deg 1.274 r_angle_other_deg 1.227 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 5505 Nucleic Acid Atoms 573 Solvent Atoms 24 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing