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Crystal structure of MurC from Pseudomonas aeruginosa in complex with inhibitor M17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8EWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.50 M ammonium sulfate, 0.1 M HEPES pH 7.5. PsaeA.00137.b.B5.PW37941 at 22.5 mg/mL. Overnight soak with 5mM compound M17 in 1.0 M ammonium sulfate, 0.1M Hepes 7.5. plate 14333 well B8 drop 1. Puck: PSL-1208, Cryo: 2.5M ammonium sulfate + 5mM M17
Crystal Properties Matthews coefficient Solvent content 5.77 78.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.711 α = 90 b = 108.711 β = 90 c = 265.044 γ = 90
Symmetry Space Group I 41 2 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 EIGER2 XE 9M 2024-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
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 2.63 132.52 100 0.237 0.245 0.065 0.998 10.7 14 24139
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 2.63 2.7 100 3.104 3.211 0.815 0.657 15.1
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 2.63 68.56 1.33 24098 1246 99.92 0.2062 0.2047 0.2081 0.2329 0.2294
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 13.784 f_angle_d 0.825 f_chiral_restr 0.049 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2296 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing