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Crystal structure of MurA from Clostridium difficile, mutation C116S, in the presence of URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 10% PEG 8000, 1M NMe4Cl, 100 mM MOPS.
Crystals were then soaked in 10% PEG 8000, 1M NMe4Cl, 5 mM PEP, 200 mM NaCl, 100 mM MOPS before data collection
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.951 α = 90 b = 137.951 β = 90 c = 137.951 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9981 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 50 99.5 0.079 0.081 0.018 28.9 13.8 47699
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.2 0.44 0.485 0.198 0.009 2.9 5.6
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 (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 6q03 1.8 34.51 38120 2128 99.51 0.19034 0.1884 0.1951 0.22587 0.2314 RANDOM 31.241
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.57 r_dihedral_angle_4_deg 20.477 r_dihedral_angle_3_deg 15.558 r_long_range_B_refined 6.814 r_long_range_B_other 6.813 r_dihedral_angle_1_deg 6.147 r_scangle_other 6.034 r_scbond_it 3.942 r_scbond_other 3.941 r_mcangle_it 3.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.57 r_dihedral_angle_4_deg 20.477 r_dihedral_angle_3_deg 15.558 r_long_range_B_refined 6.814 r_long_range_B_other 6.813 r_dihedral_angle_1_deg 6.147 r_scangle_other 6.034 r_scbond_it 3.942 r_scbond_other 3.941 r_mcangle_it 3.344 r_mcangle_other 3.344 r_mcbond_it 2.404 r_mcbond_other 2.404 r_angle_refined_deg 1.521 r_angle_other_deg 0.496 r_chiral_restr 0.067 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3106 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing