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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 1SIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 PEG 3350, magnesium nitrate, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.521 α = 90 b = 78.506 β = 90 c = 94.509 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 315 2003-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.1271 ALS 8.2.2
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 1.8 90 98.8 0.069 20 4.9 39997 39997 32.6
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 1.8 1.86 99.7 0.325 5.7 4.9 3975
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 MOLECULAR REPLACEMENT THROUGHOUT 1SIX 1.8 60.86 37906 37906 2016 98.83 0.17 0.16973 0.16823 0.1804 0.19765 0.2095 RANDOM 24.076
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] -1.03 0.91 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.532 r_scangle_it 4.863 r_scbond_it 2.974 r_mcangle_it 1.996 r_angle_refined_deg 1.949 r_mcbond_it 1.136 r_angle_other_deg 0.915 r_symmetry_vdw_other 0.313 r_nbd_other 0.262 r_symmetry_vdw_refined 0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.532 r_scangle_it 4.863 r_scbond_it 2.974 r_mcangle_it 1.996 r_angle_refined_deg 1.949 r_mcbond_it 1.136 r_angle_other_deg 0.915 r_symmetry_vdw_other 0.313 r_nbd_other 0.262 r_symmetry_vdw_refined 0.262 r_symmetry_hbond_refined 0.258 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.124 r_nbtor_other 0.083 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3037 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing