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Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Orthorhombic P form2)
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 6.5 291 Morpheus H4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Inhibitor added but not bound. plate 13512 well H4 drop 2. Puck: PSL-1715, Cryo: direct
Crystal Properties Matthews coefficient Solvent content 2.29 46.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.796 α = 90 b = 63.192 β = 90 c = 119.988 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 9M 2023-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 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 2.3 43.51 99.9 0.153 0.167 0.064 0.992 8.2 6.7 20187
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 2.38 100 0.983 1.061 0.396 0.777 7.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 42.65 1.34 20112 969 99.71 0.2153 0.2133 0.2571 0.2357
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 13.846 f_angle_d 0.475 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3160 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing