2AEN

Crystal structure of the rotavirus strain DS-1 VP8* core


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6293PEG 4000, sodium chloride, sodium citrate, ethanol, tris, EDTA, sodium azide, benzamidine, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.7238.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.421α = 90.03
b = 84.123β = 90.02
c = 90.769γ = 75.54
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Mirrors2003-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.9160CHESSF1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.614.8896.80.0517.21.9515346615346619.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6694.70.3763.41.7215018

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 1KQR1.60414.8814569714569777611000.159610.159610.15790.19173RANDOM24.907
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]
0.35-0.060.07-0.13-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.543
r_dihedral_angle_3_deg11.706
r_dihedral_angle_4_deg7.243
r_dihedral_angle_1_deg6.684
r_scangle_it2.495
r_scbond_it1.789
r_angle_other_deg1.506
r_angle_refined_deg1.31
r_mcangle_it1.019
r_mcbond_it0.794
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.543
r_dihedral_angle_3_deg11.706
r_dihedral_angle_4_deg7.243
r_dihedral_angle_1_deg6.684
r_scangle_it2.495
r_scbond_it1.789
r_angle_other_deg1.506
r_angle_refined_deg1.31
r_mcangle_it1.019
r_mcbond_it0.794
r_symmetry_vdw_other0.205
r_nbd_refined0.192
r_nbd_other0.185
r_nbtor_refined0.182
r_mcbond_other0.177
r_symmetry_vdw_refined0.165
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.139
r_chiral_restr0.084
r_nbtor_other0.084
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10616
Nucleic Acid Atoms
Solvent Atoms1724
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing