7LOV

Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and noeuromycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UQM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629585 mM Sodium Citrate pH 5.6, 170 mM Ammonium Acetate, 25.5 % (w/v) PEG 4000, 15 %(v/v) Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.755.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.589α = 90
b = 82.676β = 92.43
c = 113.227γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9790NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.528.9799.90.270.996.2748863
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5899.91.790.51.37.1

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 REPLACEMENTTHROUGHOUT5UQM2.528.9746524233499.90.210.20810.2478RANDOM39.964
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]
2.5-0.21-1.21-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.275
r_dihedral_angle_4_deg16.53
r_dihedral_angle_3_deg15.513
r_dihedral_angle_1_deg5.779
r_angle_refined_deg1.219
r_angle_other_deg1.125
r_chiral_restr0.044
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.275
r_dihedral_angle_4_deg16.53
r_dihedral_angle_3_deg15.513
r_dihedral_angle_1_deg5.779
r_angle_refined_deg1.219
r_angle_other_deg1.125
r_chiral_restr0.044
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8808
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing