4U60

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with GM1 oligosaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4U5Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293100 mM Na-malonate pH 5.0, 10% PEG 3350, 10 mM GM1 oligosaccharide
Crystal Properties
Matthews coefficientSolvent content
2.4249.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.99α = 90
b = 152.05β = 90
c = 67.97γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.55099.4165.523831521.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.54995.3

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 REPLACEMENTTHROUGHOUT4U5Z1.5502264921194899.430.158740.157640.17994RANDOM17.962
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]
0.02-0.380.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.584
r_dihedral_angle_4_deg19.792
r_dihedral_angle_3_deg11.352
r_dihedral_angle_1_deg6.136
r_long_range_B_refined5.75
r_long_range_B_other5.75
r_angle_refined_deg1.419
r_scangle_other1.344
r_scbond_it0.887
r_scbond_other0.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.584
r_dihedral_angle_4_deg19.792
r_dihedral_angle_3_deg11.352
r_dihedral_angle_1_deg6.136
r_long_range_B_refined5.75
r_long_range_B_other5.75
r_angle_refined_deg1.419
r_scangle_other1.344
r_scbond_it0.887
r_scbond_other0.886
r_angle_other_deg0.83
r_mcangle_it0.797
r_mcangle_other0.797
r_mcbond_it0.48
r_mcbond_other0.479
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms10436
Nucleic Acid Atoms
Solvent Atoms1637
Heterogen Atoms323

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
Cootmodel building
XSCALEdata scaling