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Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001175 (WYH77)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9S8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1 M Sodium HEPES pH 7.5, 28% (w/v) PEG 400, 0.2 M Calcium chloride dihydrate
Crystal Properties Matthews coefficient Solvent content 2.8 56.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.83 α = 90 b = 98.79 β = 90 c = 194.16 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 PILATUS3 X 6M 2026-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 2.4 51.6 99.8 0.153 0.162 0.051 0.998 11.8 9.8 46580
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 2.4 2.48 100 2.299 2.419 0.746 0.395 10.2
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 2.4 51.6 44308 2211 99.64 0.19529 0.19235 0.1958 0.2559 0.2585 RANDOM 55.93
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] -1.41 1.21 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.56 r_long_range_B_refined 10.368 r_long_range_B_other 10.367 r_scangle_other 7.868 r_dihedral_angle_2_deg 7.771 r_dihedral_angle_1_deg 6.895 r_mcangle_it 6.42 r_mcangle_other 6.419 r_scbond_other 5.279 r_scbond_it 5.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.56 r_long_range_B_refined 10.368 r_long_range_B_other 10.367 r_scangle_other 7.868 r_dihedral_angle_2_deg 7.771 r_dihedral_angle_1_deg 6.895 r_mcangle_it 6.42 r_mcangle_other 6.419 r_scbond_other 5.279 r_scbond_it 5.278 r_mcbond_it 4.31 r_mcbond_other 4.31 r_angle_refined_deg 1.401 r_angle_other_deg 0.507 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 6979 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction