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Crystal structure of Mycobacterium tuberculosis dUTPase STOP138T mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HZA PDB entry 3HZA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.3 M Ammonium sulfate, 50 mM Tris-HCl, 12 % Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.591 α = 90 b = 54.591 β = 90 c = 83.051 γ = 120
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 mirrors 2008-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.97861 EMBL/DESY, HAMBURG X12
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 1.8 20 99.7 0.067 17.77 5.52 13306 -3 28.165
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 1.8 1.85 99.2 0.503 2.85 4.15 972
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3HZA 1.8 19.44 11999 638 96.92 0.16623 0.16423 0.20611 0.1928 RANDOM 15.958
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] 0.08 0.04 0.08 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.01 r_dihedral_angle_4_deg 21.334 r_dihedral_angle_3_deg 12.003 r_dihedral_angle_1_deg 6.754 r_scangle_it 4.179 r_scbond_it 2.705 r_mcangle_it 1.693 r_angle_refined_deg 1.549 r_mcbond_it 1.017 r_angle_other_deg 0.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.01 r_dihedral_angle_4_deg 21.334 r_dihedral_angle_3_deg 12.003 r_dihedral_angle_1_deg 6.754 r_scangle_it 4.179 r_scbond_it 2.705 r_mcangle_it 1.693 r_angle_refined_deg 1.549 r_mcbond_it 1.017 r_angle_other_deg 0.616 r_mcbond_other 0.324 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1006 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 37
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling