7B6T

Sheep Polyomavirus VP1 in complex with 10 mM globo-N-tetraose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y61 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293KSCN, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.5665.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.274α = 90
b = 130.274β = 90
c = 222.145γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-F2019-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00004SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.748.9199.90.1070.99813.515.7846279227.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.81.0850.4851.61

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6Y611.70148.908458240455099.9510.1440.14330.165122.373
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]
-2.032-2.0324.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.195
r_dihedral_angle_4_deg24.061
r_dihedral_angle_3_deg11.507
r_dihedral_angle_1_deg7.446
r_lrange_it5.153
r_lrange_other4.854
r_scangle_it2.983
r_scangle_other2.983
r_angle_other_deg2.543
r_mcangle_it2.493
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20328
Nucleic Acid Atoms
Solvent Atoms3203
Heterogen Atoms411

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building