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Crystal structure of MurE from E.coli in complex with minifrag succinimide
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
11.6% PEG4K
18.4% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.258 α = 96.824 b = 58.291 β = 91.36 c = 74.633 γ = 104.993
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 2019-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 47.61 99.7 0.1 0.998 10.2 6.6 68240
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 96.7 0.823 0.599 1.2 3.6
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 2.09 47.61 68208 3496 99.534 0.186 0.183 0.1847 0.2361 0.2312 41.526
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] -0.159 2.354 0.502 0.721 0.994 -2.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.682 r_dihedral_angle_4_deg 15.557 r_dihedral_angle_3_deg 13.866 r_lrange_it 7.229 r_lrange_other 7.229 r_dihedral_angle_1_deg 6.831 r_scangle_it 5.936 r_scangle_other 5.936 r_mcangle_it 4.22 r_mcangle_other 4.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.682 r_dihedral_angle_4_deg 15.557 r_dihedral_angle_3_deg 13.866 r_lrange_it 7.229 r_lrange_other 7.229 r_dihedral_angle_1_deg 6.831 r_scangle_it 5.936 r_scangle_other 5.936 r_mcangle_it 4.22 r_mcangle_other 4.22 r_scbond_it 3.952 r_scbond_other 3.951 r_mcbond_it 3.059 r_mcbond_other 3.056 r_angle_refined_deg 1.487 r_angle_other_deg 1.331 r_symmetry_xyhbond_nbd_refined 0.341 r_nbd_refined 0.205 r_nbd_other 0.205 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_other 0.175 r_symmetry_xyhbond_nbd_other 0.158 r_nbtor_refined 0.152 r_symmetry_nbd_refined 0.133 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.068 r_xyhbond_nbd_other 0.013 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 320 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing