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Structure of 9N-I DNA polymerase incorporation with 3'-AL 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 3.82 67.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.654 α = 90 b = 207.654 β = 90 c = 207.654 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 2017-02-22 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 3.3 48.99 96.1 0.04456 0.991 6.73 1.9 21653
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 3.301 3.419 0.47 0.654
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 3.3 48.99 20521 1129 96.13 0.21867 0.21538 0.2152 0.27881 0.2682 RANDOM 97.998
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 26.592 r_dihedral_angle_3_deg 16.245 r_dihedral_angle_4_deg 11.385 r_long_range_B_refined 6.68 r_long_range_B_other 6.679 r_dihedral_angle_1_deg 5.602 r_scangle_other 2.197 r_mcangle_it 2.172 r_mcangle_other 2.172 r_scbond_it 1.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.592 r_dihedral_angle_3_deg 16.245 r_dihedral_angle_4_deg 11.385 r_long_range_B_refined 6.68 r_long_range_B_other 6.679 r_dihedral_angle_1_deg 5.602 r_scangle_other 2.197 r_mcangle_it 2.172 r_mcangle_other 2.172 r_scbond_it 1.232 r_scbond_other 1.231 r_mcbond_it 1.206 r_mcbond_other 1.205 r_angle_refined_deg 1.189 r_angle_other_deg 1.146 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 5563 Nucleic Acid Atoms 611 Solvent Atoms 26 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing