3HXI

Crystal structure of Schistosome eIF4E complexed with m7GpppG 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 DROP6.5277100mM pH 6.5 Mops, 20% PEG4K, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1542.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.311α = 90
b = 125.33β = 90
c = 37.33γ = 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)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
11.824422977

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 REPLACEMENTTHROUGHOUT2v8w1.82417407196994.460.223550.218310.27158RANDOM23.342
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]
-0.38-11.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.598
r_dihedral_angle_4_deg14.068
r_dihedral_angle_3_deg12.815
r_dihedral_angle_1_deg6.063
r_scangle_it3.328
r_scbond_it2.17
r_mcangle_it1.523
r_angle_refined_deg1.348
r_mcbond_it1.003
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.598
r_dihedral_angle_4_deg14.068
r_dihedral_angle_3_deg12.815
r_dihedral_angle_1_deg6.063
r_scangle_it3.328
r_scbond_it2.17
r_mcangle_it1.523
r_angle_refined_deg1.348
r_mcbond_it1.003
r_nbtor_refined0.306
r_symmetry_vdw_refined0.199
r_nbd_refined0.192
r_symmetry_hbond_refined0.104
r_xyhbond_nbd_refined0.101
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms1645
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms52

Software

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