6HNJ

The ligand-bound, open structure of CD0873, a substrate binding protein with adhesive properties from Clostridium difficile.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1 M MES pH 6.5, with 2% each of PEG 400, 500 MME, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000 and 10,000
Crystal Properties
Matthews coefficientSolvent content
2.3948.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.963α = 90
b = 57.534β = 90
c = 148.526γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.874.2699.90.2370.250.0770.993719.831122
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)
11.81.8498.31.4831.5610.4830.7211.820

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.874.2629490154699.960.205930.204140.23898RANDOM30.663
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]
2.690.12-2.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.956
r_dihedral_angle_4_deg14.866
r_dihedral_angle_3_deg14.624
r_long_range_B_refined5.881
r_long_range_B_other5.865
r_dihedral_angle_1_deg5.858
r_scangle_other4.557
r_scbond_it2.88
r_scbond_other2.877
r_mcangle_other2.847
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.956
r_dihedral_angle_4_deg14.866
r_dihedral_angle_3_deg14.624
r_long_range_B_refined5.881
r_long_range_B_other5.865
r_dihedral_angle_1_deg5.858
r_scangle_other4.557
r_scbond_it2.88
r_scbond_other2.877
r_mcangle_other2.847
r_mcangle_it2.846
r_mcbond_it1.904
r_mcbond_other1.895
r_angle_refined_deg1.557
r_angle_other_deg0.934
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms2218
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing