6HNK

The ligand-free, open 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 6HNI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.2 M potassium chloride, 7.5% PEG 6000, 7.5% PEG 8,000, 7.5% PEG 10,000
Crystal Properties
Matthews coefficientSolvent content
2.7154.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.394α = 90
b = 62.254β = 90
c = 146.102γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

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
12.5146.195.90.1580.1770.0790.9986.2812793
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)
12.52.6180.20.6730.7960.3440.7821.97.7

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 REPLACEMENTTHROUGHOUT6HNI2.573.051181993995.310.255050.250540.31012RANDOM66.741
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]
6.860.44-7.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.459
r_dihedral_angle_4_deg17.56
r_dihedral_angle_3_deg15.332
r_long_range_B_other7.572
r_long_range_B_refined7.57
r_dihedral_angle_1_deg6.354
r_mcangle_it5.412
r_mcangle_other5.41
r_scangle_other4.726
r_mcbond_it3.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.459
r_dihedral_angle_4_deg17.56
r_dihedral_angle_3_deg15.332
r_long_range_B_other7.572
r_long_range_B_refined7.57
r_dihedral_angle_1_deg6.354
r_mcangle_it5.412
r_mcangle_other5.41
r_scangle_other4.726
r_mcbond_it3.34
r_mcbond_other3.339
r_scbond_it2.736
r_scbond_other2.735
r_angle_refined_deg1.28
r_angle_other_deg0.893
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms2200
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing