4V4J
Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VSA | 1VSA, 2OW8. PROTEINS L15, L19, L21, L28 AND L29 FROM PDB ENTRY 2J03. |
experimental model | PDB | 2OW8 | 1VSA, 2OW8. PROTEINS L15, L19, L21, L28 AND L29 FROM PDB ENTRY 2J03. |
experimental model | PDB | 2J03 | 1VSA, 2OW8. PROTEINS L15, L19, L21, L28 AND L29 FROM PDB ENTRY 2J03. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 298 | Buffer conditions: 25 mM K-HEPES (pH 7.5), 12.5 mM Na-cacodylate pH 5.5, 2.5 mM Tris-HCl (pH 7.5), 80 mM NH_4 Cl, 80 mM KCl, 11 mM MgCl_2, 6.5 mM Thermine HCl and 0.2 M KSCN. Crystallization by the hanging drop method over 26-30% MPD in the above buffer mix, using 2 uL of ribosome complex mixed with 2 uL of well mixture on siliconized cover slips, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.454 | 72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 507.21 | α = 90 |
b = 507.21 | β = 90 |
c = 692.51 | γ = 90 |
Symmetry | |
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Space Group | I 4 2 2 |
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 315 | 2004-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 12.3.1 | 0.9835 | ALS | 12.3.1 |
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 | 3.83 | 78 | 82 | 0.15 | 354761 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | THROUGHOUT | 1VSA, 2OW8. PROTEINS L15, L19, L21, L28 AND L29 FROM PDB ENTRY 2J03. | 3.83 | 30 | 346189 | 10068 | 81.68 | 0.327 | 0.327 | 0.351 | RANDOM |
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] | |
-0.05 | -0.05 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.383 |
r_dihedral_angle_3_deg | 18.93 |
r_dihedral_angle_4_deg | 15.665 |
r_dihedral_angle_1_deg | 3.429 |
r_angle_refined_deg | 1.237 |
r_symmetry_vdw_refined | 0.41 |
r_nbd_refined | 0.316 |
r_nbtor_refined | 0.302 |
r_symmetry_hbond_refined | 0.277 |
r_xyhbond_nbd_refined | 0.227 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 26862 |
Nucleic Acid Atoms | 64786 |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
CNS | refinement |
d*TREK | data reduction |
SCALA | data scaling |
CNS | phasing |