4CI7 | pdb_00004ci7

The crystal structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer associated protein of Clostridium difficile


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.2 M AMMONIUM SULPHATE, 30% (V/V) PEG 4000, PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.1943.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.91α = 90
b = 73.49β = 93.57
c = 125.63γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-08-09MSINGLE WAVELENGTH
21x-rayPIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795, 0.9793, 0.9795DiamondI02
2SYNCHROTRONDIAMOND BEAMLINE I030.9717, 0.9879DiamondI03

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
11.448.1593.90.099164.8170213
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)
11.41.4265.30.2584.22.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUTNONE1.4125.39156435831090.720.13970.138140.140.169090.17RANDOM17.361
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]
2.15-0.28-1.04-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.293
r_sphericity_free31.904
r_dihedral_angle_4_deg20.132
r_dihedral_angle_3_deg12.904
r_dihedral_angle_1_deg11.447
r_sphericity_bonded11.413
r_long_range_B_refined4.099
r_long_range_B_other3.716
r_scangle_other3.198
r_scbond_it2.731
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.293
r_sphericity_free31.904
r_dihedral_angle_4_deg20.132
r_dihedral_angle_3_deg12.904
r_dihedral_angle_1_deg11.447
r_sphericity_bonded11.413
r_long_range_B_refined4.099
r_long_range_B_other3.716
r_scangle_other3.198
r_scbond_it2.731
r_scbond_other2.731
r_rigid_bond_restr2.543
r_mcangle_it2.006
r_mcangle_other2.006
r_mcbond_it1.629
r_mcbond_other1.608
r_angle_refined_deg1.34
r_angle_other_deg0.853
r_chiral_restr0.094
r_gen_planes_refined0.009
r_bond_refined_d0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7127
Nucleic Acid Atoms
Solvent Atoms927
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
CRANKphasing