3HXG

Crystal structure of Schistsome eIF4E complexed with m7GpppA and 4E-BP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V8W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5279100mM pH 6.5 Mops, 20% PEG4K, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
2.1643.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.56α = 90
b = 125.4β = 90
c = 37.34γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12008-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.5ALS4.2.2

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
12.132.080.1133.68

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 REPLACEMENTTHROUGHOUT2v8w2.13211767129699.650.21550.209710.2687RANDOM19.898
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]
-0.06-0.410.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.219
r_dihedral_angle_4_deg14.625
r_dihedral_angle_3_deg12.479
r_dihedral_angle_1_deg5.932
r_scangle_it3.115
r_scbond_it2.091
r_mcangle_it1.37
r_angle_refined_deg1.222
r_mcbond_it0.945
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.219
r_dihedral_angle_4_deg14.625
r_dihedral_angle_3_deg12.479
r_dihedral_angle_1_deg5.932
r_scangle_it3.115
r_scbond_it2.091
r_mcangle_it1.37
r_angle_refined_deg1.222
r_mcbond_it0.945
r_nbtor_refined0.299
r_symmetry_vdw_refined0.201
r_nbd_refined0.183
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.115
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.004
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_refined
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 Atoms1618
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms51

Software

Software
Software NamePurpose
PHASESphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling