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X-ray Crystal Structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E8C PDB ENTRY 1E8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MORPHEUS SCREEN CONDITION D9 0.1 M TRIS/BICINE, PH 8.5, 30% (W/V) PEG550MME/PEG20K MIX, 0.12 M 1,6 HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL (RACEMIC), 2-PROPANOL, 1,4-BUTANEDIOL, 1,3-PROANEDIOL MIX)
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.54 α = 90 b = 54.29 β = 91.6 c = 71.19 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 53 89.2 0.07 11.1 3.06 50122 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 54.9 0.39 2.5 2.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1E8C 1.8 52.23 48057 2065 88.9 0.16167 0.16016 0.195 0.19716 0.2284 RANDOM 22.008
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] 0.38 -0.07 -0.15 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_4_deg 19.689 r_dihedral_angle_3_deg 13.561 r_dihedral_angle_1_deg 5.929 r_scangle_it 3.605 r_scbond_it 2.252 r_angle_refined_deg 1.54 r_mcangle_it 1.23 r_mcbond_it 0.715 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_4_deg 19.689 r_dihedral_angle_3_deg 13.561 r_dihedral_angle_1_deg 5.929 r_scangle_it 3.605 r_scbond_it 2.252 r_angle_refined_deg 1.54 r_mcangle_it 1.23 r_mcbond_it 0.715 r_chiral_restr 0.119 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3810 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing