3L28

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain K339A mutant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2.82930.1M SODIUM CITRATE, 0.3M LITHIUM SULFATE, 13% PEG8000, pH 2.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.381α = 90
b = 91.88β = 99.6
c = 102.595γ = 90
Symmetry
Space GroupP 1 21 1

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
12.45099.80.044293.83819038190
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)
12.42.421000.4332.83.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3FKE2.433.773196031958172087.910.203520.199870.26908RANDOM9.914
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]
-0.20.010.150.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.749
r_dihedral_angle_3_deg13.949
r_dihedral_angle_4_deg11.144
r_dihedral_angle_1_deg4.401
r_scangle_it2.27
r_mcangle_it1.903
r_scbond_it1.492
r_mcbond_it1.197
r_angle_refined_deg0.873
r_nbtor_refined0.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.749
r_dihedral_angle_3_deg13.949
r_dihedral_angle_4_deg11.144
r_dihedral_angle_1_deg4.401
r_scangle_it2.27
r_mcangle_it1.903
r_scbond_it1.492
r_mcbond_it1.197
r_angle_refined_deg0.873
r_nbtor_refined0.291
r_nbd_refined0.158
r_symmetry_vdw_refined0.143
r_xyhbond_nbd_refined0.105
r_symmetry_hbond_refined0.079
r_chiral_restr0.055
r_metal_ion_refined0.044
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms5637
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms67

Software

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