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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 2OWQ
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 2.78 55.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.62 α = 90 b = 92.62 β = 90 c = 145.86 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 plus toroidal mirror 2012-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9763 ESRF ID23-1
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 1.85 48.62 99.9 0.072 15.8 7.1 61990 61957
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 1.85 1.95 99.9 0.542 3.5 7
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 2OWQ 1.85 46.31 61990 58772 3132 99.86 0.1773 0.17518 0.1833 0.21832 0.2277 RANDOM 37.112
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.376 r_dihedral_angle_3_deg 16.33 r_dihedral_angle_4_deg 15.086 r_long_range_B_other 6.991 r_long_range_B_refined 6.989 r_dihedral_angle_1_deg 6.939 r_scangle_other 4.096 r_scbond_it 2.885 r_scbond_other 2.833 r_mcangle_it 2.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.376 r_dihedral_angle_3_deg 16.33 r_dihedral_angle_4_deg 15.086 r_long_range_B_other 6.991 r_long_range_B_refined 6.989 r_dihedral_angle_1_deg 6.939 r_scangle_other 4.096 r_scbond_it 2.885 r_scbond_other 2.833 r_mcangle_it 2.558 r_mcangle_other 2.529 r_angle_refined_deg 2.201 r_mcbond_it 1.788 r_mcbond_other 1.783 r_angle_other_deg 1.072 r_chiral_restr 0.155 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.003 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 4386 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 42
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling