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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Uric acid, Form III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WRV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 293 0.1 M Bis-Tris pH 5.5, 0.5 M Sodium citrate, 25% PEG (w/v) 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.37 α = 90 b = 60.02 β = 90 c = 74.47 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 IMAGE PLATE RIGAKU RAXIS IV 2021-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.88 30.01 91.35 0.0459 0.985 8.82 2 16264
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.947 0.327 0.902
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 4WRV 1.88 30.01 15185 812 91.37 0.21028 0.20751 0.217 0.26457 0.2652 RANDOM 23.734
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] -0.32 0.1 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.311 r_dihedral_angle_4_deg 24.456 r_dihedral_angle_3_deg 15.695 r_dihedral_angle_1_deg 6.865 r_long_range_B_refined 6.413 r_long_range_B_other 6.393 r_scangle_other 3.805 r_mcangle_other 2.89 r_mcangle_it 2.889 r_scbond_it 2.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.311 r_dihedral_angle_4_deg 24.456 r_dihedral_angle_3_deg 15.695 r_dihedral_angle_1_deg 6.865 r_long_range_B_refined 6.413 r_long_range_B_other 6.393 r_scangle_other 3.805 r_mcangle_other 2.89 r_mcangle_it 2.889 r_scbond_it 2.377 r_scbond_other 2.376 r_mcbond_it 1.908 r_mcbond_other 1.903 r_angle_refined_deg 1.536 r_angle_other_deg 1.311 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 1684 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing