5DFE
70S termination complex containing E. coli RF2
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 5.5% PEG 20k, 11% PEG 200, 100 mM TRIS-ACETATE, 200 mM KSCN, 10 mM MAGNESIUM ACETATE 2.8 mM DOBC |
2 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 5.8% PEG 20k, 11.6% PEG 200, 200 mM TRIS-ACETATE, 200 mM KSCN, 10 mM MAGNESIUM ACETATE 2.8mM DOBC |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.29 | 62.6 |
3.29 | 62.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 210.48 | α = 90 |
b = 450.41 | β = 90 |
c = 622.55 | 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 | 2015-07-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9792 | 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 | 3.09997551079 | 49.9 | 99 | 0.269 | 0.994 | 8.98 | 12.7 | 1057161 | -3 | 65.1513074296 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.1 | 3.18 | 99.9 | 1.002 | 0.577 | 1.82 |
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 | 3.09997551079 | 49.8846320819 | 1.36291542291 | 1057107 | 49510 | 99.9591504427 | 0.197081129841 | 0.195631996396 | 0.227251785283 | Inherited | 77.0700635802 |
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 | 14.0328978407 |
f_angle_d | 0.916861275819 |
f_chiral_restr | 0.0464920157642 |
f_plane_restr | 0.00764910354419 |
f_bond_d | 0.0047503827355 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 97165 |
Nucleic Acid Atoms | 196956 |
Solvent Atoms | |
Heterogen Atoms | 2541 |
Software
Software | |
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Software Name | Purpose |
PHENIX | phasing |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |