7K1U

Crystal Structure of SrtB-anchored Collagen-binding Adhesin Fragment (residues 206-565) from Clostridioides difficile strain 630


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5292Protein: 9.3 mg/ml 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: Classics II (G7), 0.2M Ammonium acetate, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1861.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.323α = 90
b = 69.323β = 90
c = 187.527γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBE2020-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.4301000.090.090.0960.0360.997227.221161-349.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.441000.8340.8340.8960.3260.8781.87.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.429.6420033107499.810.17590.17370.2173RANDOM52.26
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]
1.160.581.16-3.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.458
r_dihedral_angle_3_deg9.219
r_dihedral_angle_4_deg8.687
r_dihedral_angle_1_deg3.796
r_angle_refined_deg1.426
r_angle_other_deg0.345
r_chiral_restr0.055
r_gen_planes_refined0.054
r_gen_planes_other0.052
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.458
r_dihedral_angle_3_deg9.219
r_dihedral_angle_4_deg8.687
r_dihedral_angle_1_deg3.796
r_angle_refined_deg1.426
r_angle_other_deg0.345
r_chiral_restr0.055
r_gen_planes_refined0.054
r_gen_planes_other0.052
r_bond_refined_d0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1945
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing