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Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 1.9M ammonium sulfate, 7% (v/v) PEG 400, 0.1M Hepes 7.5. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 2mM A19 in crystallant (10 ul) for 2h, and transferred to another 10 ul of the same solution for another 2h. plate Liu-Lim-116 A2. Puck: PSL-0401, Cryo: 2.5M Lithium Sulfate + 2mM inhibitor A19
Crystal Properties Matthews coefficient Solvent content 3.02 59.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.488 α = 90 b = 65.488 β = 90 c = 134.764 γ = 90
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 2024-04-13 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 1.35 67.38 100 0.069 0.072 0.019 1 17.7 13.5 124023
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 1.35 1.39 100 1.317 1.388 0.435 0.682 10
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 1.35 58.9 1.34 123930 6027 99.98 0.1339 0.1327 0.1446 0.1575 0.1661
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 12.379 f_angle_d 0.919 f_chiral_restr 0.079 f_plane_restr 0.011 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3260 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 131
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing