5J3C
Thermus thermophilus 70S termination complex containing E. coli RF1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 5.2% PEG 20k, 10.4% PEG 200, 100 mM TRIS-ACETATE, 200 mM KSCN, 10 mM MAGNESIUM ACETATE 2.8 mM DOBC |
2 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 4.0% PEG 20k, 8.0% PEG 200, 200 mM TRIS-ACETATE, 200 mM KSCN, 10 mM MAGNESIUM ACETATE 2.8mM DOBC |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 209.51 | α = 90 |
b = 450.89 | β = 90 |
c = 622.07 | 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 | 2 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | S/N 60-0112-F | 2015-12-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97910 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 3.04 | 49.87 | 99.3 | 0.346 | 0.989 | 6.46 | 12.7 | 1109069 | -3 | 65.17 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.04 | 3.12 | 98.5 | 1.985 | 1.59 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4Y4O | 3.04 | 49.864 | 1.33 | 1109007 | 52113 | 99.35 | 0.2479 | 0.2465 | 0.2785 | Inherited | 82.1372 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.149 |
f_angle_d | 0.895 |
f_chiral_restr | 0.05 |
f_bond_d | 0.005 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 95535 |
Nucleic Acid Atoms | 196930 |
Solvent Atoms | |
Heterogen Atoms | 2464 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PHENIX | refinement |
PDB_EXTRACT | data extraction |