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Uracil-DNA glycosylase from Micrococcus flavus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Sodium HEPES pH 7.5, 10% v/v 2-Propanol, 20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.276 α = 90 b = 43.722 β = 95.32 c = 84.511 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS EIGER X 4M 2022-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9679 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.482 42.073 79.8 0.119 0.13 0.051 8.2 6.2 28705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.482 1.584 22.2 1.095 1.21 0.505 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.71 42.073 22046 1142 98.75 0.16641 0.16453 0.179 0.20255 0.2162 RANDOM 24.257
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] 0.59 0.07 -0.3 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.916 r_dihedral_angle_2_deg 7.756 r_dihedral_angle_1_deg 6.267 r_long_range_B_refined 5.726 r_long_range_B_other 5.595 r_scangle_other 3.308 r_scbond_other 2.114 r_scbond_it 2.113 r_angle_refined_deg 1.593 r_mcangle_it 1.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.916 r_dihedral_angle_2_deg 7.756 r_dihedral_angle_1_deg 6.267 r_long_range_B_refined 5.726 r_long_range_B_other 5.595 r_scangle_other 3.308 r_scbond_other 2.114 r_scbond_it 2.113 r_angle_refined_deg 1.593 r_mcangle_it 1.566 r_mcangle_other 1.566 r_mcbond_it 1.099 r_mcbond_other 1.095 r_angle_other_deg 0.585 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1726 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction