4EGT

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.52890.1 M sodium acetate, 1.1 M succinic acid, 1.0% PEG2000 MME, pH 5.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.7730.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.93α = 90
b = 88.144β = 90
c = 135.599γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252010-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.99985SSRFBL17U

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
125099.10.08929.83.73620735882-2
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)
122.0399.90.2318.33.91727

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 2GH8236.953620733925178998.750.200730.200730.199160.23154RANDOM22.745
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]
0.19-0.220.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.447
r_dihedral_angle_4_deg15.477
r_dihedral_angle_3_deg12.307
r_scangle_it5.338
r_dihedral_angle_1_deg3.964
r_scbond_it3.441
r_mcangle_it2.327
r_mcbond_it1.362
r_angle_refined_deg1.245
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.447
r_dihedral_angle_4_deg15.477
r_dihedral_angle_3_deg12.307
r_scangle_it5.338
r_dihedral_angle_1_deg3.964
r_scbond_it3.441
r_mcangle_it2.327
r_mcbond_it1.362
r_angle_refined_deg1.245
r_chiral_restr0.089
r_gen_planes_refined0.011
r_bond_refined_d0.008
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 Atoms4870
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling