3TCQ

Crystal Structure of matrix protein VP40 from Ebola virus Sudan


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1729111mg/ml EbsuA.17247.a PD00181, 10% PEG4000, 20% glycerol, 0.1M MES pH 6.5. Direct cryoprotection. , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1442.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.982α = 90
b = 90.94β = 95.86
c = 48.684γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

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
11.627.36899.40.06610.82136225
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)
11.61.6699.70.4822.481

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4DUT1.627.36834411180899.190.195820.194480.22052RANDOM38.075
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]
4.1-3.56-3.47-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.665
r_dihedral_angle_3_deg15.181
r_dihedral_angle_4_deg10.77
r_dihedral_angle_1_deg6.562
r_angle_refined_deg1.59
r_angle_other_deg0.812
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.665
r_dihedral_angle_3_deg15.181
r_dihedral_angle_4_deg10.77
r_dihedral_angle_1_deg6.562
r_angle_refined_deg1.59
r_angle_other_deg0.812
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1791
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling