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Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20 N-terminus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 293 100 mM bicine, 1.5 M ammonium sulfate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.98 α = 90 b = 92.98 β = 90 c = 145.71 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r Si111 monochromator and toroidal mirror 2012-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9394 ESRF ID14-4
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 2.2 54.02 99.7 0.075 13.2 5.3 37537 37537
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 2.2 2.32 99.9 0.516 4 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4OD8 2.2 44.29 37537 35622 1873 99.57 0.19634 0.19382 0.197 0.245 0.2478 RANDOM 47.682
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] -0.02 -0.01 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.762 r_dihedral_angle_3_deg 19.006 r_dihedral_angle_4_deg 16.37 r_dihedral_angle_1_deg 7.135 r_long_range_B_other 6.101 r_long_range_B_refined 6.1 r_scangle_other 3.3 r_mcangle_it 2.526 r_mcangle_other 2.524 r_scbond_it 2.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.762 r_dihedral_angle_3_deg 19.006 r_dihedral_angle_4_deg 16.37 r_dihedral_angle_1_deg 7.135 r_long_range_B_other 6.101 r_long_range_B_refined 6.1 r_scangle_other 3.3 r_mcangle_it 2.526 r_mcangle_other 2.524 r_scbond_it 2.263 r_scbond_other 2.212 r_angle_refined_deg 1.994 r_mcbond_it 1.686 r_mcbond_other 1.672 r_angle_other_deg 1.009 r_chiral_restr 0.129 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 4361 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 42
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling