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Crystal Structure of M. tuberculosis MenD bound to Mg2+ and covalent intermediate I (a ThDP and decarboxylated 2-oxoglutarate adduct)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 10% PEG 4K, 20% Glycerol, 0.02M CA, pH 7.5 (MORPHEUS G7) [CA=carboxylic acid mix, buffer=MOPS/HEPES-Na]
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.144 α = 90 b = 143.551 β = 90 c = 174.289 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 110 CCD ADSC QUANTUM 315r 2012-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.2 19.73 99.4 0.111 0.043 0.999 15.3 7.5 128138 45.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 99.3 2.007 0.773 0.443 1.2 7.6 6271
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.2 19.726 1.33 128035 5427 99.37 0.1884 0.1863 0.1842 0.2286 0.2287 52.2799
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 16.269 f_angle_d 0.934 f_chiral_restr 0.05 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15960 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 126
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data scaling REFMAC refinement PHASER phasing