2IL9
Crystal Structure of Plautia Stali Intestine Virus Intergenic Region Internal Ribosome Entry Site Ribosomal Binding Domain RNA at 3.1 Angstroms
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 303 | 15% MPD, 150 mM MgAcetate, 0.5 mM Spermidine; cryoprotected with 20% MPD, 150 mM MgAcetate, 50 mM Na-MES pH 5.6, 5 mM Iridium (III) hexammine, vapor diffusion, sitting drop, temperature 303K |
2 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 303 | 15% MPD, 100 mM MgAcetate, 0.5 mM Spermidine; cryoprotected with 20% MPD, 100 mM MgAcetate, 50 mM Na-MES pH 5.6, 5% isopropanol, vapor diffusion, sitting drop, temperature 303K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 133.57 | α = 90 |
b = 133.57 | β = 90 |
c = 160.425 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | ADSC QUANTUM 210 | 2006-04-25 | M | MAD | ||||||
2 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2006-05-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.1053,1.1057,1.1004 | ALS | 8.2.1 |
2 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.1 | 16.97 | 26973 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 3.1 | 16.97 | 26973 | 2683 | 92.4 | 0.253 | 0.294 | RANDOM | 87.6 |
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] | |
-1.15 | 13.95 | -1.15 | 2.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 15.1 |
c_improper_angle_d | 1.39 |
c_angle_deg | 1 |
c_bond_d | 0.005 |
c_mcbond_it | |
c_mcangle_it | |
c_scbond_it | |
c_scangle_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 5665 |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SOLVE | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |