7LOU

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295200 mM Ammonium phosphate monobasic, 20% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.550.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.087α = 90
b = 121.34β = 90
c = 206.417γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2019-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
11.82121.3499.80.070.9913.87.3115828
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)
11.821.8597.81.60.6216

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 REPLACEMENTTHROUGHOUT5UQM1.82104.61109893582699.750.21720.21540.2515RANDOM43.184
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]
2.841.26-4.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.767
r_dihedral_angle_4_deg21.764
r_dihedral_angle_3_deg15.345
r_dihedral_angle_1_deg6.466
r_angle_refined_deg1.412
r_angle_other_deg1.315
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.767
r_dihedral_angle_4_deg21.764
r_dihedral_angle_3_deg15.345
r_dihedral_angle_1_deg6.466
r_angle_refined_deg1.412
r_angle_other_deg1.315
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8851
Nucleic Acid Atoms
Solvent Atoms487
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing