4HEA
Crystal structure of the entire respiratory complex I from Thermus thermophilus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 295 | 100 mM Bis-Tris pH 6.0, 19% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 2.2 mM FOS-CHOLINE-8 fluorinated , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
2 | VAPOR DIFFUSION, SITTING DROP | 6 | 295 | 100 mM Bis-Tris pH 6.0, 24% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 50 mM NDSB-201, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
3 | VAPOR DIFFUSION, SITTING DROP | 6 | 295 | 100 mM Bis-Tris pH 6.0, 26% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.6% DDM, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.28 | α = 90 |
b = 340.89 | β = 100.57 |
c = 263.3 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | mirrors | 2011-09-23 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | PIXEL | PSI PILATUS 6M | mirrors | 2011-12-03 | M | SINGLE WAVELENGTH | |||||
3 | 3 | x-ray | 100 | PIXEL | PSI PILATUS 6M | mirrors | 2011-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.9 | ESRF | ID29 |
2 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.9 | ESRF | ID29 |
3 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.9 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||
1,2,3 | 3.3 | 40 | 99.5 | 0.251 | 0.251 | 5.1 | 6.1 | 247920 | 247920 | 99 |
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) | ||||||||||
1,2,3 | 3.3 | 3.48 | 99 | 1.869 | 1.869 | 1 | 5.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | THROUGHOUT | PDB entries 3I9V and 4HE8 | 3.3027 | 39.998 | 233383 | 233383 | 2427 | 93.66 | 0.2034 | 0.2024 | 0.2393 | Random, using lattice symmetry information (PHENIX). | 74.4 |
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 | 18.03 |
f_angle_d | 1.467 |
f_chiral_restr | 0.111 |
f_bond_d | 0.008 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 73808 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 190 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |