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Crystal structure of MurA from Clostridium difficile, mutation C116D, n the presence of UDP-N-acetylmuramic 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, 1 M NMe4Cl, 200 mM NaCl, 100 mM MOPS
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.409 α = 90 b = 139.409 β = 90 c = 139.409 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 0.9987 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.65 50 99.1 0.055 80.3 20.9 53427
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 89.1 0.39 4.8 11.1
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 1.65 29.74 50734 2693 99.61 0.1707 0.169 0.1785 0.1998 0.2048 RANDOM 27.509
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 38.807 r_dihedral_angle_4_deg 17.258 r_dihedral_angle_3_deg 14.489 r_dihedral_angle_1_deg 6.324 r_angle_refined_deg 1.732 r_angle_other_deg 1.618 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_4_deg 17.258 r_dihedral_angle_3_deg 14.489 r_dihedral_angle_1_deg 6.324 r_angle_refined_deg 1.732 r_angle_other_deg 1.618 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3111 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing