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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Orotic 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 6.5 293 0.1 M Bis-Tris pH 6.5, 25% PEG (w/v) 3350
Crystal Properties Matthews coefficient Solvent content 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.58 α = 90 b = 59.7 β = 90 c = 75.07 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 2020-10-02 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 2 46.73 96.44 0.033 0.995 13.57 2 14172
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 2 2.072 0.169 0.903
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WRV 2 46.73 13510 662 96.45 0.16997 0.16757 0.22079 0.2245 RANDOM 20.472
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] -0.63 -0.66 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 21.051 r_dihedral_angle_3_deg 12.297 r_dihedral_angle_1_deg 6.678 r_long_range_B_refined 5.922 r_long_range_B_other 5.852 r_scangle_other 3.629 r_mcangle_it 2.766 r_mcangle_other 2.765 r_scbond_it 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 21.051 r_dihedral_angle_3_deg 12.297 r_dihedral_angle_1_deg 6.678 r_long_range_B_refined 5.922 r_long_range_B_other 5.852 r_scangle_other 3.629 r_mcangle_it 2.766 r_mcangle_other 2.765 r_scbond_it 2.33 r_scbond_other 2.328 r_angle_other_deg 2.296 r_mcbond_it 1.832 r_mcbond_other 1.826 r_angle_refined_deg 1.599 r_chiral_restr 0.075 r_bond_other_d 0.035 r_gen_planes_other 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 1691 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing