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Crystal structure of E.coli MurE - C269S C340S C450S in complex with Ellman's reagent
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 0.1M citrate pH 5.5
13% PEG4K
19.5% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.59 α = 96.72 b = 58.94 β = 91.48 c = 74.38 γ = 104.47
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 S 6M 2020-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.68 56.6 97 0.999 12.1 3.6 105615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.72 0.384
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7B53 1.68 56.6 105607 5286 96.981 0.199 0.197 0.2037 0.2392 0.2435 37.212
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] -0.626 0.715 0.036 0.226 1.149 -0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.527 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 12.886 r_lrange_it 7.244 r_lrange_other 7.228 r_dihedral_angle_1_deg 6.702 r_scangle_it 6.011 r_scangle_other 6.01 r_mcangle_other 4.013 r_mcangle_it 4.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.527 r_dihedral_angle_4_deg 16.521 r_dihedral_angle_3_deg 12.886 r_lrange_it 7.244 r_lrange_other 7.228 r_dihedral_angle_1_deg 6.702 r_scangle_it 6.011 r_scangle_other 6.01 r_mcangle_other 4.013 r_mcangle_it 4.012 r_scbond_it 3.988 r_scbond_other 3.988 r_mcbond_it 2.931 r_mcbond_other 2.928 r_angle_refined_deg 1.543 r_angle_other_deg 1.375 r_symmetry_xyhbond_nbd_refined 0.228 r_nbd_refined 0.208 r_symmetry_nbd_other 0.172 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.156 r_nbd_other 0.153 r_symmetry_nbd_refined 0.142 r_symmetry_xyhbond_nbd_other 0.141 r_xyhbond_nbd_other 0.113 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7217 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing