4V81
The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Q3Q | PDB entry 1Q3Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | Prior to crystallisation CCT was complexed to alpha-Actin and Plp2 and purified as described (Altschuler et al., 2009, Febs Letters, 583, 782-786) and crystallised in hanging drops in the presence of ATP and Beryllium Fluoride, which was added as BeSO4 and KF. Equilibration buffer contained 100 mM Hepes pH 7.6, 50 mM MgCl2, 300 mM Na2SeO4, 6% PEG8k,1.0 mM TCEP, and 20% glycerol. Note that in the drop, protein at 4.3 mg/ml was mixed with equal amounts of equilibration buffer lacking glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 159.1 | α = 85.23 |
b = 162.54 | β = 81.15 |
c = 268.1 | γ = 61.17 |
Symmetry | |
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Space Group | P 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 | 2008-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0001 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.8 | 90 | 91.6 | 0.077 | 8.4 | 1.86 | 392007 | 209755 | 1 | 1 | 112 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.8 | 4 | 93.2 | 0.392 | 1.92 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | PDB entry 1Q3Q | 3.8 | 89.946 | 1.99 | 392007 | 209673 | 10483 | 91.56 | 0.3089 | 0.307 | 0.3443 | 5% (XDSCONV) |
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] | |
17.1038 | 8.2778 | 32.079 | -7.3146 | 6.802 | -9.7892 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.414 |
f_angle_d | 0.678 |
f_chiral_restr | 0.043 |
f_bond_d | 0.003 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 55221 |
Nucleic Acid Atoms | |
Solvent Atoms | 4 |
Heterogen Atoms | 418 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
PHENIX | refinement |
XDS | data reduction |