3L26

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 DROP4.72932.9M SODIUM FORMATE, 0.1M SODIUM CITRATE, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.025α = 90
b = 81.025β = 90
c = 90.249γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12009-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.20.979ALS4.2.2

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
12.4501000.1521.3141229712297
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)
12.42.421000.8763.813.6

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 3FKE2.448.39116231162358299.630.18260.18260.179060.25407RANDOM4.678
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]
-0.12-0.120.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.678
r_dihedral_angle_4_deg18.302
r_dihedral_angle_3_deg14.584
r_dihedral_angle_1_deg5.472
r_angle_refined_deg1.215
r_mcangle_it0.308
r_nbtor_refined0.291
r_scangle_it0.186
r_nbd_refined0.177
r_mcbond_it0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.678
r_dihedral_angle_4_deg18.302
r_dihedral_angle_3_deg14.584
r_dihedral_angle_1_deg5.472
r_angle_refined_deg1.215
r_mcangle_it0.308
r_nbtor_refined0.291
r_scangle_it0.186
r_nbd_refined0.177
r_mcbond_it0.177
r_symmetry_hbond_refined0.175
r_symmetry_vdw_refined0.14
r_xyhbond_nbd_refined0.132
r_scbond_it0.121
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1910
Nucleic Acid Atoms168
Solvent Atoms233
Heterogen Atoms10

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling