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Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase, Form IV
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 citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.65 53.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.71 α = 90 b = 63.91 β = 90 c = 86.47 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 MAR scanner 345 mm plate 2014-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
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 1.9 43.24 99.7 0.263 7.4 12.5 20588
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 1.9 2 99.2 0.931 2.7 12.2
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 1.9 43.24 19489 1054 99.66 0.16534 0.1634 0.1755 0.20181 0.217 RANDOM 20.39
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] 0.72 -0.17 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.3 r_dihedral_angle_4_deg 21.503 r_dihedral_angle_3_deg 13.009 r_long_range_B_refined 6.336 r_long_range_B_other 6.335 r_dihedral_angle_1_deg 5.838 r_scangle_other 4.078 r_scbond_it 2.601 r_scbond_other 2.601 r_mcangle_it 2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.3 r_dihedral_angle_4_deg 21.503 r_dihedral_angle_3_deg 13.009 r_long_range_B_refined 6.336 r_long_range_B_other 6.335 r_dihedral_angle_1_deg 5.838 r_scangle_other 4.078 r_scbond_it 2.601 r_scbond_other 2.601 r_mcangle_it 2.52 r_mcangle_other 2.52 r_angle_refined_deg 1.886 r_mcbond_it 1.675 r_mcbond_other 1.673 r_angle_other_deg 0.949 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1682 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing