3L25

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain bound to 8 bp dsRNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FKEPDB ENTRY 3FKE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22933M SODIUM FORMATE, 0.1M SODIUM CITRATE, 5% GLYCEROL, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4148.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.947α = 90
b = 84.571β = 90
c = 89.316γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
12501000.12115.94.84113541135
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)
22.031000.7582.24.7

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 3FKE244.683901239012203899.70.171290.171290.169380.20744RANDOM17.138
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_deg32.192
r_dihedral_angle_4_deg18.88
r_dihedral_angle_3_deg13.732
r_dihedral_angle_1_deg4.773
r_scangle_it2.474
r_scbond_it1.577
r_angle_other_deg1.241
r_angle_refined_deg1.226
r_mcangle_it0.875
r_mcbond_it0.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.192
r_dihedral_angle_4_deg18.88
r_dihedral_angle_3_deg13.732
r_dihedral_angle_1_deg4.773
r_scangle_it2.474
r_scbond_it1.577
r_angle_other_deg1.241
r_angle_refined_deg1.226
r_mcangle_it0.875
r_mcbond_it0.471
r_symmetry_vdw_other0.299
r_nbtor_refined0.297
r_symmetry_vdw_refined0.211
r_nbd_other0.204
r_nbd_refined0.191
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.136
r_metal_ion_refined0.097
r_chiral_restr0.078
r_nbtor_other0.069
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3862
Nucleic Acid Atoms336
Solvent Atoms335
Heterogen Atoms94

Software

Software
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling