6HNI

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1 M sodium HEPES pH 7.5, 20% (w/v) PEG 10,000
Crystal Properties
Matthews coefficientSolvent content
2.2946.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.107α = 90
b = 42.351β = 94.76
c = 56.175γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.3555.9899.90.2970.3090.0860.9979.72567816
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)
11.351.3798.86.4556.882.3190.3271.717

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 REPLACEMENTTHROUGHOUT3LKV1.3555.9865622210699.990.149620.148490.18547RANDOM19.074
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]
-0.042.09-1.070.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.29
r_sphericity_free31.765
r_sphericity_bonded14.604
r_dihedral_angle_3_deg11.128
r_dihedral_angle_1_deg5.505
r_long_range_B_refined3.801
r_long_range_B_other3.506
r_scangle_other3.091
r_dihedral_angle_4_deg2.856
r_scbond_other2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.29
r_sphericity_free31.765
r_sphericity_bonded14.604
r_dihedral_angle_3_deg11.128
r_dihedral_angle_1_deg5.505
r_long_range_B_refined3.801
r_long_range_B_other3.506
r_scangle_other3.091
r_dihedral_angle_4_deg2.856
r_scbond_other2.67
r_scbond_it2.668
r_rigid_bond_restr2.659
r_mcangle_it2.601
r_mcangle_other2.6
r_mcbond_other2.018
r_mcbond_it2.017
r_angle_refined_deg1.802
r_angle_other_deg1.046
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2196
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing