4EJR

Crystal structure of major capsid protein S domain from rabbit hemorrhagic disease virus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72890.2 M magnesium chloride, 0.1 M HEPES sodium, 30% PEG400, pH 7.0, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.7931.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.734α = 90
b = 48.362β = 100.95
c = 65.163γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

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
125099.770.08625.77.42487224815-2
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)
122.0799.80.4043.976.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2GH8249.352487224813133099.790.202570.20050.24064RANDOM23.968
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]
0.010.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.424
r_dihedral_angle_3_deg15.48
r_dihedral_angle_4_deg14.489
r_dihedral_angle_1_deg6.654
r_scangle_it5.925
r_scbond_it3.82
r_mcangle_it2.631
r_angle_refined_deg2.109
r_mcbond_it1.559
r_chiral_restr0.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.424
r_dihedral_angle_3_deg15.48
r_dihedral_angle_4_deg14.489
r_dihedral_angle_1_deg6.654
r_scangle_it5.925
r_scbond_it3.82
r_mcangle_it2.631
r_angle_refined_deg2.109
r_mcbond_it1.559
r_chiral_restr0.172
r_bond_refined_d0.027
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2520
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms

Software

Software
Software NamePurpose
SERGUIdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling