2DWR

Crystal structure of the human Wa rotavirus VP8* carbohydrate-recognising domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherHomology model based on the structure of porcine CRW-8 VP8* that we have solved.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629525% PEG 4000, 20% 2-propanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0759.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.762α = 90
b = 74.762β = 90
c = 70.09γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2004-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9794ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.564.68135

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHomology model based on the structure of porcine CRW-8 VP8* that we have solved.2.564.5528114749135596.540.179730.177180.23508RANDOM31.888
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]
1.360.681.36-2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.678
r_dihedral_angle_3_deg16.865
r_dihedral_angle_4_deg12.765
r_dihedral_angle_1_deg6.653
r_scangle_it1.973
r_scbond_it1.193
r_angle_refined_deg1.106
r_mcangle_it0.949
r_mcbond_it0.528
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.678
r_dihedral_angle_3_deg16.865
r_dihedral_angle_4_deg12.765
r_dihedral_angle_1_deg6.653
r_scangle_it1.973
r_scbond_it1.193
r_angle_refined_deg1.106
r_mcangle_it0.949
r_mcbond_it0.528
r_nbtor_refined0.307
r_symmetry_vdw_refined0.206
r_nbd_refined0.197
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.115
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1300
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XNEMOdata collection
FIPdata collection
MOSFLMdata reduction
CCP4data scaling
AMoREphasing