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Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-nitrouracil, Form I
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 2.12 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.024 α = 90 b = 64.117 β = 112.46 c = 45.131 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 CCD MARMOSAIC 225 mm CCD 2014-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
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 1.18 32.07 99.8 0.101 7.9 3.7 67385
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 1.18 1.24 98.8 0.481 2.4 3.4
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 3A7N 1.18 32.07 63908 3406 99.79 0.13093 0.12913 0.16407 0.1838 RANDOM 12.051
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] -0.52 -0.07 0.37 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.867 r_sphericity_free 34.305 r_dihedral_angle_4_deg 20.348 r_dihedral_angle_3_deg 12.001 r_sphericity_bonded 9.384 r_dihedral_angle_1_deg 5.804 r_long_range_B_refined 4.465 r_rigid_bond_restr 4.364 r_long_range_B_other 3.645 r_mcangle_it 3.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.867 r_sphericity_free 34.305 r_dihedral_angle_4_deg 20.348 r_dihedral_angle_3_deg 12.001 r_sphericity_bonded 9.384 r_dihedral_angle_1_deg 5.804 r_long_range_B_refined 4.465 r_rigid_bond_restr 4.364 r_long_range_B_other 3.645 r_mcangle_it 3.412 r_mcangle_other 3.411 r_scangle_other 3.04 r_mcbond_it 2.625 r_mcbond_other 2.611 r_scbond_it 2.536 r_scbond_other 2.534 r_angle_refined_deg 1.76 r_angle_other_deg 0.959 r_chiral_restr 0.289 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 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 1734 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing