3ASS

Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with Lewis-b


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop4.6298PEG 6000, hexanediol, pH 4.6, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.69α = 90
b = 74.69β = 90
c = 106.973γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102008-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
11.65099.90.04325.511.28851388432
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)
11.61.631000.23810.44445

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 REPLACEMENTTHROUGHOUT3ASR1.631.2383912443599.810.185650.18480.20171RANDOM20.002
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.883
r_dihedral_angle_4_deg11.803
r_dihedral_angle_3_deg11.705
r_dihedral_angle_1_deg5.767
r_scangle_it2.157
r_scbond_it1.298
r_angle_refined_deg1.075
r_mcangle_it1.001
r_mcbond_it0.532
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.883
r_dihedral_angle_4_deg11.803
r_dihedral_angle_3_deg11.705
r_dihedral_angle_1_deg5.767
r_scangle_it2.157
r_scbond_it1.298
r_angle_refined_deg1.075
r_mcangle_it1.001
r_mcbond_it0.532
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4703
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms112

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling