6YLR
Translation initiation factor 4E in complex with bn7GpppG mRNA 5' cap analog
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1L8B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 9 | 291 | 0.1 M Bis-Tris propane pH 9.0, 0.1 M NaCl, 25 % w/v PEG 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.047 | α = 90 |
b = 94.047 | β = 90 |
c = 42.446 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 | PIXEL | DECTRIS PILATUS 6M | 2017-05-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.195 | 42.06 | 99.42 | 0.1473 | 0.1596 | 0.06037 | 0.995 | 11.01 | 7 | 19244 | 37.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.195 | 2.274 | 96.92 | 0.8653 | 0.9346 | 0.3486 | 0.805 | 1.99 | 7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | NONE | 1L8B | 2.1954544917 | 42.06 | 1.37750892456 | 19183 | 961 | 99.4401534394 | 0.226350871249 | 0.224039294544 | 0.269553771557 | 58.3221400192 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 9.62705472716 |
f_angle_d | 0.760719641553 |
f_chiral_restr | 0.0485318648276 |
f_bond_d | 0.00315135333631 |
f_plane_restr | 0.00279147244875 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2756 |
Nucleic Acid Atoms | |
Solvent Atoms | 192 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |