4BEA

Crystal Structure of eIF4E in Complex with a Stapled Peptide Derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AZAPDB ENTRY 4AZA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.518-26% OF POLYETHYLENE GLYCOL 3350, 0.01-02M AMMONIUM SULPHATE AND 100MM BIS-TRIS AT PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.4249.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.301α = 90
b = 91.677β = 90
c = 137.908γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMIRRORS2012-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER X8 PROTEUM

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
12.5768.9598.80.0911.0810.158036-3
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)
12.572.6383.20.462.332.64

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 4AZA2.5745.88764037198.880.222320.220250.26575RANDOM15.144
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]
-0.360.4-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.071
r_dihedral_angle_4_deg19.858
r_dihedral_angle_3_deg16.827
r_dihedral_angle_1_deg6.932
r_angle_refined_deg1.355
r_angle_other_deg0.781
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.071
r_dihedral_angle_4_deg19.858
r_dihedral_angle_3_deg16.827
r_dihedral_angle_1_deg6.932
r_angle_refined_deg1.355
r_angle_other_deg0.781
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.003
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1601
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM2data reduction
PROTEUM2data scaling
PHASERphasing