5J4D
E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 289 | 3.1 uL 70S*mRNA*tRNAfMet complex + 3.1 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate), reservoir: 300 uL 0.5-0.7 M sodium chloride, 4-fold molar excess of E. coli release factor 1 added during complex formation |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.3 | 62.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 211.541 | α = 90 |
b = 454.397 | β = 90 |
c = 619.473 | 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 | DECTRIS PILATUS 6M | 2015-07-26 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-07-26 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-07-26 | M | SINGLE WAVELENGTH | ||||||
4 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-07-26 | M | SINGLE WAVELENGTH | ||||||
5 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2015-07-01 | M | SINGLE WAVELENGTH | ||||||
6 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2015-07-01 | M | SINGLE WAVELENGTH | ||||||
7 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2015-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9795 | SSRL | BL12-2 |
2 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9795 | SSRL | BL12-2 |
3 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9795 | SSRL | BL12-2 |
4 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9795 | SSRL | BL12-2 |
5 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.033 | APS | 23-ID-D |
6 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.033 | APS | 23-ID-D |
7 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.033 | APS | 23-ID-D |
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 | 70 | 100 | 8.28 | 37.4 | 1174254 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FREE R-VALUE | 3.1 | 49.977 | 1.35 | 1064934 | 21298 | 99.81 | 0.2221 | 0.2214 | 0.2563 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.944 |
f_angle_d | 1.072 |
f_chiral_restr | 0.045 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 97108 |
Nucleic Acid Atoms | 201010 |
Solvent Atoms | |
Heterogen Atoms | 2903 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | phasing |
Blu-Ice | data collection |