4NCL

Crystal structure of eukaryotic translation initiation factor eIF5B (517-970) from Chaetomium thermophilum in complex with GDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4N3NPDB ID 4N3N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29315 % PEG 8000, 0.5 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.9α = 90
b = 72.96β = 90
c = 199.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.826580PETRA III, EMBL c/o DESYP13 (MX1)

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
12.1299.70.05617.7956555-337.01
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)
12.122.2199.90.6312.97

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ID 4N3N2.11547.8651.3456440282899.640.21570.21390.247861.3775
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
f_dihedral_angle_d15.753
f_angle_d0.956
f_chiral_restr0.04
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6720
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms58

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction