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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WS4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 293 0.1 M Tris pH 5.5, 25% PEG (w/v) 3350
Crystal Properties Matthews coefficient Solvent content 2.02 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.16 α = 90 b = 63.68 β = 112.58 c = 45.19 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 IMAGE PLATE MAR scanner 345 mm plate 2021-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 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 1.6 30.49 93.72 0.0368 0.995 11.77 2 25418
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 1.6 1.657 0.1443 0.927
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 4WS4 1.6 30.49 24223 1196 93.73 0.15057 0.14902 0.1488 0.1816 0.1813 RANDOM 11.572
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] 0.2 0.14 0.17 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.186 r_dihedral_angle_4_deg 20.297 r_dihedral_angle_3_deg 12.902 r_dihedral_angle_1_deg 6.335 r_long_range_B_refined 4.642 r_long_range_B_other 4.393 r_scangle_other 2.7 r_angle_other_deg 2.308 r_scbond_it 1.786 r_scbond_other 1.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.186 r_dihedral_angle_4_deg 20.297 r_dihedral_angle_3_deg 12.902 r_dihedral_angle_1_deg 6.335 r_long_range_B_refined 4.642 r_long_range_B_other 4.393 r_scangle_other 2.7 r_angle_other_deg 2.308 r_scbond_it 1.786 r_scbond_other 1.785 r_angle_refined_deg 1.781 r_mcangle_it 1.559 r_mcangle_other 1.559 r_mcbond_it 1.003 r_mcbond_other 0.995 r_chiral_restr 0.093 r_bond_other_d 0.034 r_gen_planes_other 0.019 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 1739 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing