6QNQ
70S ribosome initiation complex (IC) with experimentally assigned potassium ions
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4V6G |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | Tris-OAc, KSCN, PEG-20K, PEG-550mme |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.34 | 63.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 210.46 | α = 90 |
b = 452.18 | β = 90 |
c = 626.12 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | PIXEL | PSI PILATUS 6M | 2008-11-10 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2017-12-13 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2017-12-13 | M | SINGLE WAVELENGTH | ||||||
4 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2017-12-13 | M | SINGLE WAVELENGTH | ||||||
5 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2017-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.000 | SLS | X06SA |
2 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 3.351 | Diamond | I23 |
3 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 3.542 | Diamond | I23 |
4 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 3.531 | Diamond | I23 |
5 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 3.542 | Diamond | I23 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 3.5 | 226.09 | 96.7 | 0.285 | 0.177 | 7.13 | 12.36 | 719306 | 97.49 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.5 | 3.6 | 88.9 | 0.568 | 0.568 | 1.98 | 12.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | THROUGHOUT | 4v6g | 3.5 | 226.09 | 1.99 | 743746 | 22128 | 99.98 | 0.1893 | 0.1874 | 0.2513 | 96.6244 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 94097 |
Nucleic Acid Atoms | 202857 |
Solvent Atoms | |
Heterogen Atoms | 3553 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |