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Crystal structure of UMPK from M. tuberculosis in complex with UDP and UTP (P21212 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.7 293 1 M LiCl, 20 % (w/v) PEG 8K and 0.1 M Tris pH 8.7
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.23 α = 90 b = 165.75 β = 90 c = 125.02 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.979 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 3.08 29.95 98.7 0.292 0.995 8.2 12.3 57888 45.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.08 3.27 1.263 0.922 1.69
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NWY 3.33 29.95 1.35 43038 2138 92.29 0.1964 0.1923 0.1922 0.2743 0.2732 48.79
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 25.0717 f_angle_d 1.275 f_chiral_restr 0.0696 f_bond_d 0.0132 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18959 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 432
Software Software Software Name Purpose PHENIX refinement PHASER phasing Aimless data scaling XDS data reduction