6Y66

Structure of Goose Hemorrhagic Polyomavirus VP1 in complex with 2-O-Methyl-5-N-acetyl-alpha-D-neuraminic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293Na formate, ammonium acetate, Na citrate tribasic, Na oxamate, Na K tartrate, MES, imidazole, PEG 8000, ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.4148.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.46α = 94.232
b = 90.54β = 98.09
c = 101.22γ = 107.867
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-F2017-01-30MSINGLE 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
11.9549.5897.710.14680.9939.383.620688618.43
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)
11.952.020.76110.7012.02

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-VALUE4FMG1.9549.577206888206997.7240.1660.16520.200817.311
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]
0.879-0.053-1.350.141-1.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.982
r_dihedral_angle_4_deg18.975
r_dihedral_angle_3_deg11.479
r_dihedral_angle_1_deg7.652
r_lrange_it4.643
r_lrange_other4.643
r_scangle_it2.67
r_scangle_other2.67
r_mcangle_it2.002
r_mcangle_other2.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.982
r_dihedral_angle_4_deg18.975
r_dihedral_angle_3_deg11.479
r_dihedral_angle_1_deg7.652
r_lrange_it4.643
r_lrange_other4.643
r_scangle_it2.67
r_scangle_other2.67
r_mcangle_it2.002
r_mcangle_other2.002
r_scbond_it1.773
r_scbond_other1.773
r_angle_refined_deg1.467
r_angle_other_deg1.333
r_mcbond_it1.321
r_mcbond_other1.32
r_nbd_other0.308
r_symmetry_nbd_refined0.276
r_symmetry_xyhbond_nbd_refined0.214
r_symmetry_nbd_other0.187
r_nbd_refined0.186
r_xyhbond_nbd_refined0.168
r_nbtor_refined0.159
r_symmetry_xyhbond_nbd_other0.155
r_symmetry_nbtor_other0.081
r_chiral_restr0.068
r_ncsr_local_group_250.053
r_ncsr_local_group_210.051
r_ncsr_local_group_270.05
r_ncsr_local_group_340.049
r_ncsr_local_group_350.049
r_ncsr_local_group_60.048
r_ncsr_local_group_110.047
r_ncsr_local_group_150.047
r_ncsr_local_group_280.047
r_ncsr_local_group_330.047
r_ncsr_local_group_180.046
r_ncsr_local_group_40.045
r_ncsr_local_group_170.045
r_ncsr_local_group_20.044
r_ncsr_local_group_70.044
r_ncsr_local_group_230.044
r_ncsr_local_group_240.044
r_ncsr_local_group_300.044
r_ncsr_local_group_200.043
r_ncsr_local_group_220.043
r_ncsr_local_group_320.043
r_ncsr_local_group_370.043
r_ncsr_local_group_30.042
r_ncsr_local_group_100.042
r_ncsr_local_group_140.042
r_ncsr_local_group_190.042
r_ncsr_local_group_260.042
r_ncsr_local_group_310.042
r_ncsr_local_group_400.042
r_ncsr_local_group_360.041
r_ncsr_local_group_410.041
r_ncsr_local_group_420.041
r_ncsr_local_group_10.04
r_ncsr_local_group_90.04
r_ncsr_local_group_160.04
r_ncsr_local_group_440.039
r_ncsr_local_group_450.039
r_ncsr_local_group_290.038
r_ncsr_local_group_130.037
r_ncsr_local_group_390.036
r_ncsr_local_group_430.036
r_ncsr_local_group_80.034
r_ncsr_local_group_120.031
r_ncsr_local_group_380.031
r_ncsr_local_group_50.03
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20026
Nucleic Acid Atoms
Solvent Atoms2665
Heterogen Atoms333

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building