7D6Y

eIF4E in Complex with a Disulphide-Free Autonomous VH Domain


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528925% (w/v) PEG 6000, 0.01-02 M Ammonium Sulphate, 100mM Tris, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.2645.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 198.848α = 90
b = 45.324β = 93.192
c = 39.763γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.953700Australian SynchrotronMX1

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
11.66844.22999.40.1166.13.7412613.3
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)
11.671.760.6731.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2V8W1.66844.22641261206199.4410.1830.18150.206412.212
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]
0.47-0.2410.051-0.491
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.413
r_dihedral_angle_4_deg15.256
r_dihedral_angle_3_deg11.016
r_dihedral_angle_1_deg7.082
r_lrange_it4.241
r_lrange_other4.24
r_scangle_it1.348
r_scangle_other1.348
r_angle_other_deg1.261
r_mcangle_it1.241
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.413
r_dihedral_angle_4_deg15.256
r_dihedral_angle_3_deg11.016
r_dihedral_angle_1_deg7.082
r_lrange_it4.241
r_lrange_other4.24
r_scangle_it1.348
r_scangle_other1.348
r_angle_other_deg1.261
r_mcangle_it1.241
r_mcangle_other1.232
r_angle_refined_deg1.197
r_scbond_it0.786
r_scbond_other0.786
r_mcbond_it0.695
r_mcbond_other0.681
r_nbd_other0.228
r_nbd_refined0.182
r_symmetry_nbd_other0.174
r_symmetry_nbd_refined0.163
r_nbtor_refined0.161
r_xyhbond_nbd_refined0.147
r_symmetry_xyhbond_nbd_refined0.137
r_symmetry_nbtor_other0.073
r_chiral_restr0.052
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2484
Nucleic Acid Atoms
Solvent Atoms408
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing