4BEA
Crystal Structure of eIF4E in Complex with a Stapled Peptide Derivative
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4AZA | PDB ENTRY 4AZA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 18-26% OF POLYETHYLENE GLYCOL 3350, 0.01-02M AMMONIUM SULPHATE AND 100MM BIS-TRIS AT PH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.301 | α = 90 |
b = 91.677 | β = 90 |
c = 137.908 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MIRRORS | 2012-10-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER X8 PROTEUM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.57 | 68.95 | 98.8 | 0.09 | 11.08 | 10.15 | 8036 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.57 | 2.63 | 83.2 | 0.46 | 2.33 | 2.64 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4AZA | 2.57 | 45.88 | 7640 | 371 | 98.88 | 0.22232 | 0.22025 | 0.26575 | RANDOM | 15.144 |
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] | |
-0.36 | 0.4 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.071 |
r_dihedral_angle_4_deg | 19.858 |
r_dihedral_angle_3_deg | 16.827 |
r_dihedral_angle_1_deg | 6.932 |
r_angle_refined_deg | 1.355 |
r_angle_other_deg | 0.781 |
r_chiral_restr | 0.077 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1601 |
Nucleic Acid Atoms | |
Solvent Atoms | 28 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PROTEUM2 | data reduction |
PROTEUM2 | data scaling |
PHASER | phasing |