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Structure of D141A mutant of M.tuberculosis MenD (SEPHCHC Synthase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ESU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 6% w/v PEG8K, 12% ethylene glycol, halide mix (NaI, NaBr, NaF) 0.03M each, 0.1 M MOPS/HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.425 α = 90 b = 140.443 β = 90 c = 184.141 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 PIXEL DECTRIS EIGER X 16M 2021-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.42 49.19 100 0.269 0.275 0.053 0.999 12.4 27 100844
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.46 100 5.234 5.331 1.007 0.302 27.7
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.42 44.42 1.33 100732 5082 99.98 0.1953 0.1933 0.193 0.2335 0.2336
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 15.681 f_angle_d 0.599 f_chiral_restr 0.042 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15694 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing