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Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290.15 Protein: 20mg/mL. Reservoir: 0.1 M MES pH 6.5, and 12 % (w/v) PEG 20,000
Crystal Properties Matthews coefficient Solvent content 2.73 54.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.579 α = 90 b = 99.108 β = 90 c = 192.556 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 EIGER2 XE 16M 2025-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
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 2.3 88.28 100 0.075 0.078 0.021 0.999 20.5 13.5 52491
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 2.3 2.37 100 0.523 0.546 0.158 0.925 11.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.3 88.28 49711 2705 100 0.19102 0.18839 0.1972 0.23926 0.2405 RANDOM 45.897
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] 0.03 -0.95 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.117 r_long_range_B_other 10.666 r_long_range_B_refined 10.66 r_scangle_other 8.713 r_dihedral_angle_2_deg 7.225 r_mcangle_it 6.955 r_mcangle_other 6.954 r_dihedral_angle_1_deg 6.548 r_scbond_it 6.364 r_scbond_other 6.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.117 r_long_range_B_other 10.666 r_long_range_B_refined 10.66 r_scangle_other 8.713 r_dihedral_angle_2_deg 7.225 r_mcangle_it 6.955 r_mcangle_other 6.954 r_dihedral_angle_1_deg 6.548 r_scbond_it 6.364 r_scbond_other 6.338 r_mcbond_it 5.39 r_mcbond_other 5.39 r_angle_refined_deg 1.28 r_angle_other_deg 0.499 r_chiral_restr 0.127 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6938 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction