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Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SIR apo structure, pdb entry 7SIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 Molecular Dimensions Morpheus screen condition a6: 10% (w/V) PEG 8000, 20% (V/V) ethylene gycol: 30mM magnesium chloride and calcium chloride: 100mM MOPS / HEPES pH 7.5: AcbaC.17938.a.B1.PS02380: tray 323738a6: cryo: direct: puck: loi2-1
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.49 α = 90 b = 91.82 β = 90 c = 106.36 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 CCD RAYONIX MX-300 Beryllium Lenses 2021-12-09 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 1.5 50 100 0.062 0.066 0.998 19.03 8.094 86055 27.158
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 1.5 1.54 100 0.444 0.474 0.931 4.49 8.083
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 7SIR 1.5 45.91 1.34 86052 1999 99.96 0.1502 0.1497 0.1497 0.173 0.1736 0 31.91
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 12.7762 f_angle_d 0.9073 f_chiral_restr 0.0587 f_plane_restr 0.0073 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3283 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 42
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