☰ Navigation Tabs
Protein-DNA complex of Vaccinia virus D4 with double-stranded non-specific DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DOF PDB ENTRY 4DOF, CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 2:1 protein solution/reservoir (16% PEG6000, 0.08 M Tris, pH 8.5, 20% glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.389 α = 90 b = 92.327 β = 90 c = 142.859 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 100 PIXEL DECTRIS PILATUS 6M Mirrors 2014-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.89 56.5 97.9 0.158 0.158 6.1 3 12298 11991 29.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 3.05 99.3 0.505 0.505 2.3 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 PDB ENTRY 4DOF, CHAIN A 2.89 56.5 17647 11389 577 97.28 0.21826 0.21575 0.219 0.2652 0.2662 RANDOM 31.4
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] 0.03 0.08 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.522 r_dihedral_angle_4_deg 13.994 r_dihedral_angle_3_deg 13.732 r_long_range_B_refined 6.804 r_long_range_B_other 6.796 r_dihedral_angle_1_deg 6.114 r_scangle_other 3.981 r_mcangle_other 2.838 r_scbond_other 2.378 r_mcangle_it 1.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.522 r_dihedral_angle_4_deg 13.994 r_dihedral_angle_3_deg 13.732 r_long_range_B_refined 6.804 r_long_range_B_other 6.796 r_dihedral_angle_1_deg 6.114 r_scangle_other 3.981 r_mcangle_other 2.838 r_scbond_other 2.378 r_mcangle_it 1.861 r_scbond_it 1.781 r_angle_other_deg 1.297 r_angle_refined_deg 1.185 r_mcbond_it 1.07 r_mcbond_other 1.07 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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 3432 Nucleic Acid Atoms 445 Solvent Atoms 118 Heterogen Atoms 24
Software Software Software Name Purpose RAPD data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling