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Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with compound 8918
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L9U apo structure, PDB entry 7L9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 287 Optimization condition based on Anatrace/Calibre MCSG1 screen, condition C9: 33% (w/V) PEG 4000, 800mM lithium chloride, 100mM Tris Base/ HCl pH 8.0: MytuD.00149.b.B1.PW38903 at 35mg/ml + 5mM compound 8918: tray 319823 a10, cryo: 20% EG + 5mM compound: puck hyq3-8
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.85 α = 90 b = 100.85 β = 90 c = 49.69 γ = 120
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 RAYONIX MX-300 2021-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 50 100 0.054 0.061 0.998 15.85 4.66 52394 40.035
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 99.9 0.563 0.648 0.749 2.23 4.124
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE apo structure, PDB entry 7L9U 1.8 43.19 1.98 52371 2091 99.97 0.1901 0.1887 0.1889 0.2205 0.2168 0 41.85
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 13.5752 f_angle_d 0.7371 f_chiral_restr 0.0481 f_bond_d 0.0059 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4355 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 62
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing PHENIX model building Coot model building