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Crystal structure of MurE from E.coli in complex with Z757284380
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
11.9% PEG4K
20.1% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.409 α = 97.11 b = 58.621 β = 91.54 c = 74.438 γ = 104.841
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 I24 0.96862 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.78 56.36 97.57 0.074 0.088 0.048 0.998 8.9 3.3 88411
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.81 96.3 1.619 1.93 0.314 0.3 3.4
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 1.82 56.34 87246 4460 96.243 0.195 0.1929 0.1974 0.2311 0.2339 39.71
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] -0.332 0.914 -0.362 0.592 0.244 -0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.327 r_dihedral_angle_4_deg 19.045 r_dihedral_angle_3_deg 14.018 r_lrange_it 8.596 r_lrange_other 8.587 r_scangle_it 6.702 r_scangle_other 6.701 r_dihedral_angle_1_deg 6.528 r_mcangle_it 4.576 r_mcangle_other 4.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.327 r_dihedral_angle_4_deg 19.045 r_dihedral_angle_3_deg 14.018 r_lrange_it 8.596 r_lrange_other 8.587 r_scangle_it 6.702 r_scangle_other 6.701 r_dihedral_angle_1_deg 6.528 r_mcangle_it 4.576 r_mcangle_other 4.575 r_scbond_it 4.277 r_scbond_other 4.276 r_mcbond_it 3.17 r_mcbond_other 3.16 r_angle_refined_deg 1.505 r_angle_other_deg 1.317 r_symmetry_nbd_refined 0.241 r_nbd_other 0.206 r_nbd_refined 0.205 r_symmetry_nbd_other 0.173 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.158 r_nbtor_refined 0.152 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.012 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 7282 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing