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Crystal structure of MurE from E.coli in complex with Z1198948504
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
10% PEG4K
19.7% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.137 α = 97.08 b = 58.153 β = 91.49 c = 74.348 γ = 104.93
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 2020-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.96862 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 1.67 56.13 97.1 0.997 8.3 3.5 99570
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 1.74 1.83 0.465
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 7B53 1.67 56.13 99570 5356 96.98 0.19818 0.19668 0.2042 0.22586 0.2328 RANDOM 34.444
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] 0.24 1.07 -0.01 -0.18 0.41 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.061 r_dihedral_angle_4_deg 14.544 r_dihedral_angle_3_deg 12.377 r_long_range_B_refined 7.292 r_long_range_B_other 7.274 r_dihedral_angle_1_deg 5.504 r_scangle_other 5.496 r_mcangle_it 3.834 r_mcangle_other 3.834 r_scbond_it 3.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.061 r_dihedral_angle_4_deg 14.544 r_dihedral_angle_3_deg 12.377 r_long_range_B_refined 7.292 r_long_range_B_other 7.274 r_dihedral_angle_1_deg 5.504 r_scangle_other 5.496 r_mcangle_it 3.834 r_mcangle_other 3.834 r_scbond_it 3.542 r_scbond_other 3.542 r_mcbond_it 2.653 r_mcbond_other 2.653 r_angle_refined_deg 1.299 r_angle_other_deg 1.103 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7282 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing