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Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid, 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 8.5 293 0.1 M Tris pH 8.5, 25% PEG (w/v) 3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.28 α = 90 b = 63.91 β = 112.7 c = 45.28 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 2021-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.26 36.24 99.1 0.043 0.998 14 3.3 55586
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 1.26 1.32 0.221 0.948
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 1.26 36.26 52947 2616 99.01 0.11059 0.10899 0.1087 0.14319 0.1429 RANDOM 17.861
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] -0.16 0.82 -0.37 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.798 r_dihedral_angle_4_deg 19.708 r_dihedral_angle_3_deg 11.985 r_rigid_bond_restr 9.494 r_long_range_B_refined 6.586 r_long_range_B_other 6.276 r_dihedral_angle_1_deg 6.155 r_scangle_other 6.009 r_mcbond_it 5.732 r_mcbond_other 5.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.798 r_dihedral_angle_4_deg 19.708 r_dihedral_angle_3_deg 11.985 r_rigid_bond_restr 9.494 r_long_range_B_refined 6.586 r_long_range_B_other 6.276 r_dihedral_angle_1_deg 6.155 r_scangle_other 6.009 r_mcbond_it 5.732 r_mcbond_other 5.722 r_mcangle_it 5.495 r_mcangle_other 5.493 r_scbond_it 4.738 r_scbond_other 4.736 r_angle_refined_deg 2.022 r_angle_other_deg 1.709 r_chiral_restr 0.123 r_bond_refined_d 0.02 r_bond_other_d 0.014 r_gen_planes_refined 0.012 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1739 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing