3PA8

Structure of the C. difficile TcdB cysteine protease domain in complex with a peptide inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HO6PDB entry 3HO6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Tris HCl pH 8.0, 30% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1442.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.31α = 90
b = 45.48β = 103.53
c = 87.23γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12501000.1169.26.73344928.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111000.5342.95.84808

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 REPLACEMENTTHROUGHOUTPDB entry 3HO625031754169299.990.187590.185040.23282RANDOM35.055
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]
-0.220.61.47-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.589
r_dihedral_angle_4_deg15.314
r_dihedral_angle_3_deg13.978
r_dihedral_angle_1_deg5.523
r_scangle_it2.719
r_scbond_it1.667
r_angle_refined_deg1.304
r_mcangle_it1.076
r_mcbond_it0.56
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.589
r_dihedral_angle_4_deg15.314
r_dihedral_angle_3_deg13.978
r_dihedral_angle_1_deg5.523
r_scangle_it2.719
r_scbond_it1.667
r_angle_refined_deg1.304
r_mcangle_it1.076
r_mcbond_it0.56
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3886
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms119

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling