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Crystal structure of MurE from E.coli in complex with Z57715447
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
21% PEG4K
22% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.29 46.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.693 α = 97.098 b = 58.903 β = 91.201 c = 74.011 γ = 104.598
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 2018-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.77 73.27 95.1 0.999 8.2 1.8 87747
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 1.77 1.87 0.45
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 1.838 73.27 79052 4051 95.562 0.208 0.2057 0.2119 0.2559 0.2586 38.445
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] -0.035 1.49 -0.701 0.917 0.832 -1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.859 r_dihedral_angle_4_deg 14.953 r_dihedral_angle_3_deg 13.499 r_lrange_it 7.186 r_lrange_other 7.174 r_dihedral_angle_1_deg 6.776 r_scangle_it 5.677 r_scangle_other 5.676 r_mcangle_it 4.268 r_mcangle_other 4.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.859 r_dihedral_angle_4_deg 14.953 r_dihedral_angle_3_deg 13.499 r_lrange_it 7.186 r_lrange_other 7.174 r_dihedral_angle_1_deg 6.776 r_scangle_it 5.677 r_scangle_other 5.676 r_mcangle_it 4.268 r_mcangle_other 4.267 r_scbond_it 3.796 r_scbond_other 3.785 r_mcbond_it 3.093 r_mcbond_other 3.093 r_angle_refined_deg 1.512 r_angle_other_deg 1.328 r_symmetry_nbd_refined 0.304 r_symmetry_xyhbond_nbd_refined 0.259 r_nbd_other 0.233 r_nbd_refined 0.204 r_symmetry_nbd_other 0.174 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.154 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7215 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing