X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherHomology model based on the structure of Rhesus rotavirus VP8*

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529570% MPD, 0.1M HEPES pH 7.5, methyl-alpha-D-N-acetylneuraminide , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5952.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.929α = 90
b = 64.663β = 90
c = 109.886γ = 90
Symmetry
Space GroupP 21 21 21

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
12.355.917704

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 REPLACEMENTTHROUGHOUTHomology model based on the structure of Rhesus rotavirus VP8*2.320176581675690199.770.1830.16540.162560.21952RANDOM21.243
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]
-11.74-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.637
r_dihedral_angle_3_deg12.934
r_dihedral_angle_4_deg10.175
r_dihedral_angle_1_deg6.108
r_scangle_it1.43
r_angle_refined_deg1.06
r_scbond_it0.892
r_mcangle_it0.593
r_nbtor_refined0.306
r_mcbond_it0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.637
r_dihedral_angle_3_deg12.934
r_dihedral_angle_4_deg10.175
r_dihedral_angle_1_deg6.108
r_scangle_it1.43
r_angle_refined_deg1.06
r_scbond_it0.892
r_mcangle_it0.593
r_nbtor_refined0.306
r_mcbond_it0.306
r_nbd_refined0.187
r_symmetry_hbond_refined0.159
r_symmetry_vdw_refined0.138
r_xyhbond_nbd_refined0.123
r_metal_ion_refined0.08
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2606
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms106

Software

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