4X16

JC Mad-1 polyomavirus VP1 in complex with GD1a oligosaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NXD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8757.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.81α = 90
b = 95.58β = 110.33
c = 128.79γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-07-12MSINGLE 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
11.83099.715.45.715714822.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8598.125.3

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 REPLACEMENTTHROUGHOUT3NXD1.830149249789899.80.167660.166410.19109RANDOM19.652
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]
-0.06-0.020.36-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.256
r_dihedral_angle_4_deg14.838
r_dihedral_angle_3_deg12.074
r_long_range_B_refined6.726
r_long_range_B_other6.726
r_dihedral_angle_1_deg6.527
r_angle_refined_deg1.443
r_scangle_other0.842
r_angle_other_deg0.772
r_mcangle_it0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.256
r_dihedral_angle_4_deg14.838
r_dihedral_angle_3_deg12.074
r_long_range_B_refined6.726
r_long_range_B_other6.726
r_dihedral_angle_1_deg6.527
r_angle_refined_deg1.443
r_scangle_other0.842
r_angle_other_deg0.772
r_mcangle_it0.59
r_mcangle_other0.59
r_scbond_it0.558
r_scbond_other0.553
r_mcbond_it0.338
r_mcbond_other0.337
r_chiral_restr0.087
r_bond_refined_d0.01
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 Atoms9976
Nucleic Acid Atoms
Solvent Atoms1070
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
PHASERphasing
XDSdata reduction
XSCALEdata scaling