6Q03

Crystal structure of MurA from Clostridium difficile in the presence of UDP-N-acetyl-alpha-D-muramic acid with modified Cys116 (S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SWE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529310% PEG 8000, 1M NMe4Cl, 200 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.550.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.946α = 90
b = 138.946β = 90
c = 138.946γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352017-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.798.2597.80.087105.447927
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.8940.461.72.7

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 REPLACEMENTTHROUGHOUT3swe1.798.2545551237697.830.18440.18240.2225RANDOM21.802
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_deg42.477
r_dihedral_angle_4_deg18.419
r_dihedral_angle_3_deg15.603
r_dihedral_angle_1_deg6.195
r_angle_refined_deg1.784
r_angle_other_deg0.958
r_chiral_restr0.108
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.477
r_dihedral_angle_4_deg18.419
r_dihedral_angle_3_deg15.603
r_dihedral_angle_1_deg6.195
r_angle_refined_deg1.784
r_angle_other_deg0.958
r_chiral_restr0.108
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3119
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing