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KSHV uracil-DNA glycosylase, apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.1 M bis-tris, 0.2 M sodium chloride, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 37.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.873 α = 90 b = 43.038 β = 99.34 c = 57.387 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2016-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.5 56.63 100 0.061 0.051 0.996 13.1 3.3 7316
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.134 0.125 0.978 6.9 3.4 809
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 2J8X 2.5 56.63 7306 323 99.95 0.2074 0.2056 0.2069 0.2481 0.252 RANDOM 22.6685
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] -0.98 1.31 -1.83 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 23.071 r_dihedral_angle_3_deg 17.112 r_dihedral_angle_1_deg 5.607 r_angle_other_deg 3.51 r_mcangle_it 2.881 r_mcbond_other 2.13 r_mcbond_it 2.129 r_angle_refined_deg 1.081 r_chiral_restr 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 23.071 r_dihedral_angle_3_deg 17.112 r_dihedral_angle_1_deg 5.607 r_angle_other_deg 3.51 r_mcangle_it 2.881 r_mcbond_other 2.13 r_mcbond_it 2.129 r_angle_refined_deg 1.081 r_chiral_restr 0.042 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1852 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing