4POT

Structure of Human Polyomavirus 9 VP1 pentamer in complex with N-glycolylneuraminic acid containing 3'-sialyllactosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4POQPDB ENTRY 4POQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.1529320% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, soaked in 40 mM (N-glycolyl neuraminic acid) 3'-sialyllactosamine for 20 minutes, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0259.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.4α = 90
b = 177.65β = 90
c = 198.65γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-Fmirrors2012-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.1132.42299.40.1510.523.84211585212860-3-328.26
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1599.650.812.253.9815585

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4POQ2.1132.4222115852010371054899.310.185950.185950.183940.22428RANDOM26.366
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]
0.07-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_4_deg18.154
r_dihedral_angle_3_deg12.92
r_dihedral_angle_1_deg6.167
r_long_range_B_refined5.481
r_angle_refined_deg1.222
r_mcangle_it1.171
r_scbond_it1.127
r_mcbond_it0.673
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_4_deg18.154
r_dihedral_angle_3_deg12.92
r_dihedral_angle_1_deg6.167
r_long_range_B_refined5.481
r_angle_refined_deg1.222
r_mcangle_it1.171
r_scbond_it1.127
r_mcbond_it0.673
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20595
Nucleic Acid Atoms
Solvent Atoms2395
Heterogen Atoms636

Software

Software
Software NamePurpose
RemDAqdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling