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Crystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VWJ PDB ENTRY 2VWJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 0.1M BICINE PH 9.0, 20% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.45 α = 90 b = 98.37 β = 90 c = 116.63 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 93 CCD ADSC QUANTUM 315 MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.72 47 95.1 0.1 8.8 3.6 23740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.72 2.87 97 0.25 4.2 3.7
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 PDB ENTRY 2VWJ 2.72 47.01 22478 1229 94.12 0.23676 0.23361 0.2297 0.29455 0.2915 RANDOM 28.55
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] -0.55 -1.2 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.413 r_dihedral_angle_3_deg 14.708 r_dihedral_angle_4_deg 14.395 r_dihedral_angle_1_deg 5.075 r_scangle_it 1.55 r_angle_refined_deg 0.959 r_scbond_it 0.892 r_mcangle_it 0.801 r_angle_other_deg 0.783 r_mcbond_it 0.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.413 r_dihedral_angle_3_deg 14.708 r_dihedral_angle_4_deg 14.395 r_dihedral_angle_1_deg 5.075 r_scangle_it 1.55 r_angle_refined_deg 0.959 r_scbond_it 0.892 r_mcangle_it 0.801 r_angle_other_deg 0.783 r_mcbond_it 0.428 r_chiral_restr 0.062 r_mcbond_other 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5949 Nucleic Acid Atoms 513 Solvent Atoms 22 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing