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Crystal structure of MurE from E.coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1M citrate pH 5.5
14% PEG4K
20% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.631 α = 97.32 b = 58.944 β = 91.54 c = 74.228 γ = 105.17
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 2018-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.75 56.4 96.6 0.997 8.4 1.9 92515
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 1.75 1.8 93.5 0.495 1.3
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 1e8c 1.75 56.34 88075 4440 96.49 0.19645 0.19525 0.2032 0.21971 0.2279 RANDOM 38.196
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] -0.98 0.96 -0.17 0.93 0.6 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.743 r_dihedral_angle_4_deg 13.032 r_dihedral_angle_3_deg 12.508 r_long_range_B_refined 6.546 r_long_range_B_other 6.516 r_dihedral_angle_1_deg 5.351 r_scangle_other 4.542 r_scbond_it 3.099 r_scbond_other 3.099 r_mcangle_other 2.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.743 r_dihedral_angle_4_deg 13.032 r_dihedral_angle_3_deg 12.508 r_long_range_B_refined 6.546 r_long_range_B_other 6.516 r_dihedral_angle_1_deg 5.351 r_scangle_other 4.542 r_scbond_it 3.099 r_scbond_other 3.099 r_mcangle_other 2.936 r_mcangle_it 2.935 r_mcbond_it 2.119 r_mcbond_other 2.117 r_angle_refined_deg 1.157 r_angle_other_deg 1.043 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7284 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing