2I2O
Crystal Structure of an eIF4G-like Protein from Danio rerio
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (7% PEG 4K, 0.40 M sodium chloride, 0.1 M MES/Acetate pH 5.5) CRYOPROTECTED WITH 10% PEG 4K, 0.1 M MES/Acetate pH 5.5, 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 317.796 | α = 90 |
b = 40.948 | β = 90.26 |
c = 40.917 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | MARMOSAIC 300 mm CCD | HORIZONTAL SAGITALLY FOCUSING SECOND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR | 2006-08-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.97925 | APS | 22-ID |
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 | 1.92 | 40.612 | 97.5 | 0.074 | 13.377 | 6.4 | 39789 |
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) | |||||||||||
1.92 | 1.99 | 95.5 | 0.245 | 5.769 | 5.4 | 3895 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.92 | 40.612 | 39773 | 1998 | 97.423 | 0.192 | 0.192 | 0.19 | 0.235 | RANDOM | 8.556 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.771 | -0.37 | -0.237 | -0.537 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.124 |
r_dihedral_angle_4_deg | 21.682 |
r_dihedral_angle_3_deg | 15.162 |
r_dihedral_angle_1_deg | 5.853 |
r_scangle_it | 2.991 |
r_scbond_it | 2.001 |
r_angle_refined_deg | 1.357 |
r_mcangle_it | 1.1 |
r_mcbond_it | 0.71 |
r_symmetry_vdw_refined | 0.337 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3437 |
Nucleic Acid Atoms | |
Solvent Atoms | 418 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
HKL | data processing |
SHARP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL | data scaling |
PHENIX | phasing |
ARP/wARP | model building |