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E. faecium MurAA in complex with UDP-N-acetylmuramic acid (UNAM) and a covalent adduct of PEP with Cys119
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2.1 M DL-Malic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.55 65.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.865 α = 90 b = 168.376 β = 90 c = 316.198 γ = 90
Symmetry Space Group P 2 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 2018-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.65 49.81 99.78 0.2363 0.997 11.32 15.1 225455 63.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.749 3.063 0.368 0.93
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3r38 2.65 49.81 214123 11318 99.79 0.24195 0.24094 0.26067 0.2415 RANDOM 71.416
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] 2.01 0.48 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.15 r_dihedral_angle_3_deg 15.85 r_long_range_B_refined 11.428 r_long_range_B_other 11.428 r_scangle_other 7.982 r_dihedral_angle_1_deg 6.163 r_scbond_it 5.054 r_scbond_other 5.054 r_mcangle_it 4.352 r_mcangle_other 4.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.15 r_dihedral_angle_3_deg 15.85 r_long_range_B_refined 11.428 r_long_range_B_other 11.428 r_scangle_other 7.982 r_dihedral_angle_1_deg 6.163 r_scbond_it 5.054 r_scbond_other 5.054 r_mcangle_it 4.352 r_mcangle_other 4.352 r_mcbond_it 2.854 r_mcbond_other 2.854 r_angle_other_deg 2.28 r_angle_refined_deg 1.311 r_chiral_restr 0.06 r_bond_refined_d 0.007 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 38209 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 528
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing