4YK8
Crystal structure of the Atg101-Atg13 complex from fission yeast
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | 4M sodium chloride, 0.1M Tris-HCl pH 8.0, 0.2% D-fructose 1,6-diphosphate trisodium salt octahydrate, 0.2% glycerol phosphate disodium salt hydrate, 0.2% L-O-phosphoserine, 0.2% phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.82 | 56.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.822 | α = 90 |
b = 83.389 | β = 106.22 |
c = 91.113 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 95 | CCD | RAYONIX MX225HE | 2013-11-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0000, 1.0070 | SPring-8 | BL41XU |
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 | 43.75 | 99.2 | 0.072 | 15.7 | 3.8 | 11052 | 11052 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 3 | 3.05 | 99.6 | 2.5 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 3 | 43.74 | 10666 | 562 | 99.2 | 0.267 | 0.267 | 0.288 | RANDOM | 92.3 |
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] | |
-11.79 | 32.45 | 0.25 | 11.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24 |
c_mcangle_it | 3.02 |
c_scangle_it | 2.7 |
c_scbond_it | 1.72 |
c_mcbond_it | 1.65 |
c_angle_deg | 1.5 |
c_improper_angle_d | 0.92 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2643 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
REFMAC | refinement |
Coot | model building |
PHASES | phasing |
HKL-2000 | data processing |
HKL-2000 | data reduction |
HKL-2000 | data scaling |