6QNR
70S ribosome elongation complex (EC) with experimentally assigned potassium ions
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | Tris-OAc, KSCN, PEG-20k, PEG-550mme |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 209.46 | α = 90 |
b = 446.2 | β = 90 |
c = 623.05 | 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 | 2016-09-30 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2016-09-30 | M | SINGLE WAVELENGTH | ||||||
4 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2016-09-30 | M | SINGLE WAVELENGTH | ||||||
5 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2016-09-30 | M | SINGLE WAVELENGTH | ||||||
6 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2016-09-30 | M | SINGLE WAVELENGTH | ||||||
7 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2016-09-30 | M | SINGLE WAVELENGTH | ||||||
8 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 12M | 2016-09-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 3.351 | Diamond | I23 |
5 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 3.542 | Diamond | I23 |
6 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 3.351 | Diamond | I23 |
7 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 3.542 | Diamond | I23 |
8 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 3.351 | Diamond | I23 |
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 | 3.1 | 223.1 | 96.5 | 6.94 | 9.1 | 1043872 | 63.91 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 3.1 | 3.2 | 88.4 | 0.6 | 0.6 | 1.9 | 8.86 |
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 | THROUGHOUT | 4v6f | 3.1 | 223.1 | 2 | 1041035 | 31119 | 99.73 | 0.1981 | 0.1964 | 0.2532 | 75.7228 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 94969 |
Nucleic Acid Atoms | 207167 |
Solvent Atoms | |
Heterogen Atoms | 3589 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |