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Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-nitrouracil, Form III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 293 Sodium acetate trihydrate, Sodium cacodylate trihydrate, PEG 8000, Jeffamine M-600
Crystal Properties Matthews coefficient Solvent content 2.02 39.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.52 α = 90 b = 60.02 β = 90 c = 74.88 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 CCD MARMOSAIC 225 mm CCD 2013-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 39.52 99.6 0.067 20.3 10.6 41836
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 97.2 0.479 3.8 7
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 3A7N 1.4 39.52 39662 2114 99.45 0.12214 0.12013 0.1196 0.16033 0.1596 RANDOM 18.413
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] -0.82 0.06 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.881 r_sphericity_free 28.703 r_dihedral_angle_4_deg 19.942 r_sphericity_bonded 12.945 r_dihedral_angle_3_deg 11.171 r_dihedral_angle_1_deg 6.061 r_long_range_B_refined 5.415 r_rigid_bond_restr 4.922 r_long_range_B_other 4.853 r_scangle_other 4.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.881 r_sphericity_free 28.703 r_dihedral_angle_4_deg 19.942 r_sphericity_bonded 12.945 r_dihedral_angle_3_deg 11.171 r_dihedral_angle_1_deg 6.061 r_long_range_B_refined 5.415 r_rigid_bond_restr 4.922 r_long_range_B_other 4.853 r_scangle_other 4.751 r_mcangle_it 4.006 r_mcangle_other 4.006 r_scbond_it 3.886 r_scbond_other 3.878 r_mcbond_it 3.36 r_mcbond_other 3.357 r_angle_refined_deg 1.997 r_angle_other_deg 0.971 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1691 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing