6J0Q

Crystal structure of P domain from GII.11 swine norovirus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100mM Tris (pH 8.0), 16% (w/v) polyethylene glycol 3350, 6% (v/v) tacsimate (pH 8.0)
Crystal Properties
Matthews coefficientSolvent content
2.5150.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.237α = 90
b = 76.237β = 90
c = 241.799γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U11.0000SSRFBL17U1

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
11.9985099.90.14308.749356
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)
122.091000.4898.3

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 REPLACEMENTTHROUGHOUT3PUN25046779249799.650.181540.179740.21627RANDOM22.866
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]
-0.86-0.861.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.508
r_dihedral_angle_4_deg19.204
r_dihedral_angle_3_deg10.546
r_dihedral_angle_1_deg6.425
r_long_range_B_refined4.932
r_long_range_B_other4.439
r_scangle_other2.405
r_mcangle_it1.999
r_mcangle_other1.999
r_scbond_it1.445
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.508
r_dihedral_angle_4_deg19.204
r_dihedral_angle_3_deg10.546
r_dihedral_angle_1_deg6.425
r_long_range_B_refined4.932
r_long_range_B_other4.439
r_scangle_other2.405
r_mcangle_it1.999
r_mcangle_other1.999
r_scbond_it1.445
r_scbond_other1.444
r_angle_refined_deg1.211
r_mcbond_it1.206
r_mcbond_other1.206
r_angle_other_deg0.794
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms4741
Nucleic Acid Atoms
Solvent Atoms588
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing