4RDL

Crystal structure of Norovirus Boxer P domain in complex with Lewis y tetrasaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RDJpdb entry 4RDJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52900.1M LiCl, 18%(w/v) PEG 3350, 10%(v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.7455.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.39α = 90
b = 140.39β = 90
c = 65.02γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2012-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.0000SSRFBL17U

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
11.449501000.09527.711.112948112948122
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)
11.4491.481000.4736.111

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 REPLACEMENTTHROUGHOUTpdb entry 4RDJ1.44947.7011.35129411129411649699.980.13140.13040.1507RANDOM20.1
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]
1.62561.6256-3.2512
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.841
f_angle_d1.14
f_chiral_restr0.075
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4590
Nucleic Acid Atoms
Solvent Atoms825
Heterogen Atoms92

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling