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Mycobacterium tuberculosis dUTPase complexed with dUTP in the absence of metal ion.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other M. tuberculosis dUTPase complexed with dUMP and magnesium.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 PEG 3350, ammonium nitrate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.595 α = 90 b = 77.697 β = 90 c = 94.781 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 CCD ADSC QUANTUM 4 mirrors 2002-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 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 2.05 80 100 0.109 22.7 13.1 27903 27903 34.9
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 2.05 2.12 100 0.453 5.8 11.1 2746
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT M. tuberculosis dUTPase complexed with dUMP and magnesium. 2.1 50 23083 23083 2525 98.86 0.16959 0.16959 0.16549 0.1803 0.20675 0.2166 RANDOM 19.246
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] -0.59 -1.33 1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.375 r_scangle_it 4.932 r_scbond_it 2.921 r_angle_refined_deg 2.246 r_mcangle_it 1.791 r_angle_other_deg 1.091 r_mcbond_it 1.033 r_symmetry_vdw_other 0.353 r_nbd_other 0.265 r_symmetry_hbond_refined 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.375 r_scangle_it 4.932 r_scbond_it 2.921 r_angle_refined_deg 2.246 r_mcangle_it 1.791 r_angle_other_deg 1.091 r_mcbond_it 1.033 r_symmetry_vdw_other 0.353 r_nbd_other 0.265 r_symmetry_hbond_refined 0.19 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.163 r_nbtor_other 0.161 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2928 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing