5JIF

Crystal structure of mouse hepatitis virus strain DVIM Hemagglutinin-Esterase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherMHV-S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.1M Tris-HCl pH 8.0, 0.05M NaF, 16% w/v PEG3350, 10% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
2.7956

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.523α = 90
b = 88.819β = 90
c = 122.163γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 3152005-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9999ESRFID23-1

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
1244.4199.20.09612.59.246513942.5
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)
122.0390.91.1842.37

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 REPLACEMENTTHROUGHOUTMHV-S239.7360663326396.630.206270.205180.22595RANDOM51.651
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]
-1.115.7-4.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.505
r_dihedral_angle_4_deg15.406
r_dihedral_angle_3_deg13.766
r_dihedral_angle_1_deg6.763
r_long_range_B_refined6.134
r_long_range_B_other6.114
r_scangle_other4.112
r_scbond_it2.779
r_scbond_other2.778
r_mcangle_it2.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.505
r_dihedral_angle_4_deg15.406
r_dihedral_angle_3_deg13.766
r_dihedral_angle_1_deg6.763
r_long_range_B_refined6.134
r_long_range_B_other6.114
r_scangle_other4.112
r_scbond_it2.779
r_scbond_other2.778
r_mcangle_it2.615
r_mcangle_other2.615
r_mcbond_it1.817
r_mcbond_other1.815
r_angle_refined_deg1.468
r_angle_other_deg0.895
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5708
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms463

Software

Software
Software NamePurpose
REFMACrefinement
EVAL15data reduction
EVAL15data scaling
PHASERphasing