7XTP

eIF4E in Complex with a Disulphide-Free Autonomous VH Domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7D6Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1M Sodium HEPES pH7.5, 25% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.0539.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.623α = 90
b = 57.207β = 93.951
c = 78.963γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95373Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.82846.33299.20.14711.875926918.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8281.8997.51.6911.3

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-VALUE7D6Y1.82846.33259269306099.0590.2280.22630.259322.465
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]
1.332-0.491-0.832-0.428
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.622
r_dihedral_angle_3_deg12.496
r_dihedral_angle_other_3_deg10.802
r_dihedral_angle_4_deg10.496
r_dihedral_angle_1_deg6.853
r_lrange_it2.947
r_lrange_other2.798
r_mcangle_it1.345
r_mcangle_other1.345
r_angle_refined_deg1.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.622
r_dihedral_angle_3_deg12.496
r_dihedral_angle_other_3_deg10.802
r_dihedral_angle_4_deg10.496
r_dihedral_angle_1_deg6.853
r_lrange_it2.947
r_lrange_other2.798
r_mcangle_it1.345
r_mcangle_other1.345
r_angle_refined_deg1.172
r_scangle_it1.165
r_scangle_other1.165
r_angle_other_deg1.134
r_mcbond_it0.746
r_mcbond_other0.746
r_scbond_it0.655
r_scbond_other0.655
r_nbd_other0.19
r_symmetry_nbd_other0.17
r_nbd_refined0.167
r_nbtor_refined0.154
r_xyhbond_nbd_refined0.132
r_symmetry_nbd_refined0.128
r_symmetry_xyhbond_nbd_refined0.1
r_symmetry_nbtor_other0.07
r_chiral_restr0.041
r_bond_other_d0.006
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4849
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing