6Q11

Crystal structure of MurA from Clostridium difficile, mutation C116S, in the presence of URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q03 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729310% 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 coefficientSolvent content
2.4349.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.951α = 90
b = 137.951β = 90
c = 137.951γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2018-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9981APS19-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.75099.50.0790.0810.01828.913.847699
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)RedundancyNumber Unique Reflections (All)
11.71.7399.20.440.4850.1980.0092.95.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6q031.834.5138120212899.510.190340.18840.22587RANDOM31.241
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.57
r_dihedral_angle_4_deg20.477
r_dihedral_angle_3_deg15.558
r_long_range_B_refined6.814
r_long_range_B_other6.813
r_dihedral_angle_1_deg6.147
r_scangle_other6.034
r_scbond_it3.942
r_scbond_other3.941
r_mcangle_it3.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.57
r_dihedral_angle_4_deg20.477
r_dihedral_angle_3_deg15.558
r_long_range_B_refined6.814
r_long_range_B_other6.813
r_dihedral_angle_1_deg6.147
r_scangle_other6.034
r_scbond_it3.942
r_scbond_other3.941
r_mcangle_it3.344
r_mcangle_other3.344
r_mcbond_it2.404
r_mcbond_other2.404
r_angle_refined_deg1.521
r_angle_other_deg0.496
r_chiral_restr0.067
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3106
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing