5XCC

X-ray structure of Clostridium perfringens pili protein CppA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Sodium potassium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Imidazole, o.1M MES monohydrate (acid), 20% v/v Ethylene glycol, 10% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.4750.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.34α = 90
b = 71.33β = 90
c = 228.76γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152016-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

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
12.48114.3899.40.06816.085.2837465
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)
12.482.5498.60.493.71

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 REPLACEMENTTHROUGHOUT5XCB2.48114.3835598186799.370.229740.22750.27182RANDOM46.56
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]
0.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.312
r_dihedral_angle_3_deg11.665
r_dihedral_angle_4_deg5.65
r_dihedral_angle_1_deg5.323
r_long_range_B_refined3.359
r_long_range_B_other3.341
r_mcangle_it1.907
r_mcangle_other1.907
r_scangle_other1.786
r_mcbond_it1.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.312
r_dihedral_angle_3_deg11.665
r_dihedral_angle_4_deg5.65
r_dihedral_angle_1_deg5.323
r_long_range_B_refined3.359
r_long_range_B_other3.341
r_mcangle_it1.907
r_mcangle_other1.907
r_scangle_other1.786
r_mcbond_it1.111
r_mcbond_other1.111
r_scbond_it1.046
r_scbond_other1.046
r_angle_refined_deg0.757
r_angle_other_deg0.544
r_chiral_restr0.047
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7018
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing