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Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MQ7 pdb entry 1MQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 1.5M ammonium sulfate, 0.1M Tris/HCl, 12% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
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 IMAGE PLATE RIGAKU RAXIS II M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.49 20 94.1 4.1 24.57 3.95 21589 21589 -3 19.3
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 1.49 1.58 70.5 34.8 3.3 2.3 2595
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 1MQ7 1.49 19.44 20480 20480 1109 94.09 0.14553 0.1442 0.1497 0.16997 0.1777 RANDOM 18.838
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] 0.06 0.03 0.06 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.284 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_3_deg 9.073 r_dihedral_angle_1_deg 6.274 r_scangle_it 6.054 r_scbond_it 4.976 r_mcangle_it 3.137 r_mcbond_it 2.164 r_angle_refined_deg 1.992 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.284 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_3_deg 9.073 r_dihedral_angle_1_deg 6.274 r_scangle_it 6.054 r_scbond_it 4.976 r_mcangle_it 3.137 r_mcbond_it 2.164 r_angle_refined_deg 1.992 r_nbtor_refined 0.321 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.188 r_chiral_restr 0.148 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.108 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1081 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement START data collection XDS data reduction XSCALE data scaling MOLREP phasing