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Crystal structure of uracil-DNA glycosylase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZHX PDB ENTRY 2ZHX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 298 1.8M tri-ammonium citrate pH 7.0, 10% isopropanol, microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.84 α = 90 b = 63.67 β = 90 c = 86.4 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 mirrors 2008-08-10 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 Sym 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 1.95 30 98.2 0.1 13.7 4.8 18628 18238 1 30
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.06 97.7 0.493 3.2 4.6 2583
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2ZHX 1.95 26.24 18628 17319 885 97.74 0.18195 0.18103 0.1809 0.19888 0.2017 RANDOM 19.059
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] -0.56 0.09 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.631 r_dihedral_angle_4_deg 18.539 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 5.05 r_scangle_it 1.55 r_angle_refined_deg 1.139 r_scbond_it 0.919 r_mcangle_it 0.591 r_mcbond_it 0.337 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.631 r_dihedral_angle_4_deg 18.539 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 5.05 r_scangle_it 1.55 r_angle_refined_deg 1.139 r_scbond_it 0.919 r_mcangle_it 0.591 r_mcbond_it 0.337 r_nbtor_refined 0.301 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1764 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 26
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling