☰ Navigation Tabs
Uracil binding pocket in Vaccinia virus uracil DNA glycosylase
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 8 277 10% PEG8000, 10% DMSO, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.47 α = 90 b = 114.045 β = 90 c = 302.516 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 PSI PILATUS 6M mirrors 2013-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.77 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 2.03 49.64 95.2 0.13 0.13 25.9 17 198586 198856
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 2.03 2.14 88.9 0.584 0.584 3.9 10.2
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 2.03 49.64 198460 188435 10025 94.93 0.21455 0.21288 0.217 0.24607 0.2471 RANDOM 31.91
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.926 r_dihedral_angle_3_deg 12.12 r_dihedral_angle_4_deg 11.531 r_dihedral_angle_1_deg 5.721 r_mcangle_it 1.846 r_mcbond_it 1.091 r_mcbond_other 1.091 r_scbond_it 1.068 r_angle_refined_deg 1.049 r_angle_other_deg 0.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.926 r_dihedral_angle_3_deg 12.12 r_dihedral_angle_4_deg 11.531 r_dihedral_angle_1_deg 5.721 r_mcangle_it 1.846 r_mcbond_it 1.091 r_mcbond_other 1.091 r_scbond_it 1.068 r_angle_refined_deg 1.049 r_angle_other_deg 0.737 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_it 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 21115 Nucleic Acid Atoms Solvent Atoms 1617 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction RAPD data collection XDS data reduction SCALA data scaling PHASER phasing