6Y60

Structure of Human Polyomavirus 12 VP1 in complex with 3'-Sialyllactosamine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293Ammonium acetate, Bis-Tris, 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.5752.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.322α = 90
b = 141.724β = 90
c = 251.302γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-F2013-06-27MSINGLE 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
11.79847.3799.40.1250.99912.217.0427425133.3
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)
11.7981.911.770.7251.34

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-VALUE4FMG1.79847.37274154274199.4120.2040.20350.24330.486
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]
1.2591.898-3.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.246
r_dihedral_angle_4_deg21.357
r_dihedral_angle_3_deg12.819
r_dihedral_angle_1_deg7.175
r_lrange_it5.25
r_lrange_other5.17
r_scangle_it3.959
r_scangle_other3.959
r_mcangle_it3.217
r_mcangle_other3.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.246
r_dihedral_angle_4_deg21.357
r_dihedral_angle_3_deg12.819
r_dihedral_angle_1_deg7.175
r_lrange_it5.25
r_lrange_other5.17
r_scangle_it3.959
r_scangle_other3.959
r_mcangle_it3.217
r_mcangle_other3.217
r_scbond_it2.787
r_scbond_other2.787
r_mcbond_it2.422
r_mcbond_other2.422
r_angle_refined_deg1.629
r_angle_other_deg1.31
r_symmetry_xyhbond_nbd_refined0.47
r_symmetry_nbd_refined0.245
r_nbd_other0.213
r_nbd_refined0.199
r_symmetry_nbd_other0.187
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.154
r_symmetry_nbtor_other0.081
r_chiral_restr0.073
r_symmetry_xyhbond_nbd_other0.067
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19801
Nucleic Acid Atoms
Solvent Atoms1825
Heterogen Atoms312

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building