5YRA

Crystal Structure of Cypovirus Polyhedra R13A/S193C/A194C Mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1IN CELL300In vivo crystallization in the cytoplasm of the cell, temperature 300 K
Crystal Properties
Matthews coefficientSolvent content
1.6324.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.7α = 90
b = 103.7β = 90
c = 103.7γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7942.341006.5121.115866

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.7942.3415866174899.980.164040.158390.21784RANDOM17.521
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.478
r_dihedral_angle_4_deg18.778
r_dihedral_angle_3_deg13.989
r_dihedral_angle_1_deg6.611
r_long_range_B_refined4.659
r_long_range_B_other4.593
r_scangle_other3.281
r_scbond_it2.085
r_scbond_other2.081
r_mcangle_it2.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.478
r_dihedral_angle_4_deg18.778
r_dihedral_angle_3_deg13.989
r_dihedral_angle_1_deg6.611
r_long_range_B_refined4.659
r_long_range_B_other4.593
r_scangle_other3.281
r_scbond_it2.085
r_scbond_other2.081
r_mcangle_it2.043
r_mcangle_other2.043
r_angle_refined_deg1.754
r_mcbond_it1.342
r_mcbond_other1.341
r_angle_other_deg1.024
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1965
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing