6Y64

Structure of Sheep Polyomavirus VP1 in complex with 6'-Sialyllactosamine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Magnesium chloride, PEG 800, TRIS
Crystal Properties
Matthews coefficientSolvent content
2.4650.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.62α = 90
b = 81.26β = 115.52
c = 146.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-F2016-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00SLSX06DA

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
11.647.4796.810.0710.99917.786.835020317.04
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)
11.61.6570.7270.8212.94

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 REPLACEMENTTHROUGHOUT4FMG1.647.47346733350396.820.151970.151670.18218RANDOM18.38
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]
-0.73-0.460.340.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.913
r_dihedral_angle_4_deg20.771
r_dihedral_angle_3_deg11.426
r_dihedral_angle_1_deg7.238
r_long_range_B_refined4.631
r_long_range_B_other4.631
r_scangle_other1.813
r_mcangle_it1.545
r_mcangle_other1.545
r_angle_refined_deg1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.913
r_dihedral_angle_4_deg20.771
r_dihedral_angle_3_deg11.426
r_dihedral_angle_1_deg7.238
r_long_range_B_refined4.631
r_long_range_B_other4.631
r_scangle_other1.813
r_mcangle_it1.545
r_mcangle_other1.545
r_angle_refined_deg1.51
r_angle_other_deg1.406
r_scbond_it1.143
r_scbond_other1.143
r_mcbond_it0.91
r_mcbond_other0.909
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms19623
Nucleic Acid Atoms
Solvent Atoms2753
Heterogen Atoms366

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building