5OQ3

High resolution structure of the functional region of Cwp19 from Clostridium difficile


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28990% (10 mM monobasic potassium phosphate, 18% PEG 8,000) 10% (20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine
Crystal Properties
Matthews coefficientSolvent content
2.3748.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.016α = 90
b = 65.639β = 90
c = 104.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.3565.6499.50.1180.1230.0330.99915.425.593318
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)
11.351.371000.6740.7040.20.9823.723.7

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 REPLACEMENTTHROUGHOUT5OQ21.3555.5191316191699.440.149580.149060.17415RANDOM15.682
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]
-1.113.26-2.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.815
r_sphericity_free24.764
r_dihedral_angle_3_deg11.567
r_dihedral_angle_4_deg11.421
r_sphericity_bonded9.681
r_dihedral_angle_1_deg6.07
r_long_range_B_refined3.187
r_long_range_B_other2.962
r_scangle_other2.392
r_mcangle_other2.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.815
r_sphericity_free24.764
r_dihedral_angle_3_deg11.567
r_dihedral_angle_4_deg11.421
r_sphericity_bonded9.681
r_dihedral_angle_1_deg6.07
r_long_range_B_refined3.187
r_long_range_B_other2.962
r_scangle_other2.392
r_mcangle_other2.253
r_mcangle_it2.243
r_scbond_it2.107
r_scbond_other2.091
r_rigid_bond_restr1.881
r_mcbond_it1.793
r_mcbond_other1.766
r_angle_refined_deg1.534
r_angle_other_deg0.974
r_chiral_restr0.106
r_bond_refined_d0.013
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 Atoms2883
Nucleic Acid Atoms
Solvent Atoms385
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing