6Y64

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FMG 

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