7QLR | pdb_00007qlr

Receptor-binding protein of Clostridium difficile phage CDHS-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP278.1M HEPES pH 7, containing 0.05M ammonium acetate, 0.15M magnesium sulphate heptahydrate, 12% PEG smear medium, and 4% acetone
Crystal Properties
Matthews coefficientSolvent content
4.2771.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.99α = 90
b = 178.206β = 90
c = 227.621γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9793DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.462113.8195.80.2590.0740.9947.76.811732342.71
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.4622.7411.7720.4980.601

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)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)Mean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.462102.641.34117312588468.620.19640.19520.20.21860.248.863
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18731
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms8

Software

Software
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Auto-Rickshawphasing