7JHZ

Crystal structure of the carbohydrate-binding domain VP8* of human P[8] rotavirus strain BM13851 in complex with LNDFH I


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VKX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400,2.0 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.3347.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.192α = 90
b = 63.39β = 91.15
c = 72.26γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97930APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.6856.0895.90.1830.9777.15.113841
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.682.8297.60.6640.7645.3

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 REPLACEMENTTHROUGHOUT6VKX2.6844.781322560895.490.21350.21120.263RANDOM23.561
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]
-1.2-0.92-0.251.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.876
r_dihedral_angle_3_deg14.263
r_dihedral_angle_4_deg13.443
r_dihedral_angle_1_deg7.918
r_angle_refined_deg1.593
r_angle_other_deg1.344
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.876
r_dihedral_angle_3_deg14.263
r_dihedral_angle_4_deg13.443
r_dihedral_angle_1_deg7.918
r_angle_refined_deg1.593
r_angle_other_deg1.344
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3656
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms133

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing