3H9D
Crystal Structure of Trypanosoma brucei ATG8
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 289 | 3 uL of the protein solution (8 mg ml-1 protein in 100 mM Tris/HCl buffer, pH 6.5) with 3 uL of precipitating solution (22% v/v PEG 4000, 200 mM ammonia sulfate, 100 mM MES, pH 6.5). Droplets were equilibrated against 500 uL of precipitating solution, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.73 | 55.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.1 | α = 90 |
b = 48.6 | β = 90 |
c = 127.92 | 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 | 2008-09-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.0 | ELETTRA | 5.2R |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 25 | 13511 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.3 | 20 | 12834 | 677 | 97.22 | 0.23773 | 0.23398 | 0.30959 | RANDOM | 32.085 |
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] | |
-0.17 | -0.22 | 0.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.935 |
r_dihedral_angle_4_deg | 23.075 |
r_dihedral_angle_3_deg | 19.049 |
r_dihedral_angle_1_deg | 7.414 |
r_angle_refined_deg | 1.414 |
r_nbtor_refined | 0.297 |
r_nbd_refined | 0.191 |
r_xyhbond_nbd_refined | 0.178 |
r_symmetry_vdw_refined | 0.176 |
r_chiral_restr | 0.124 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1861 |
Nucleic Acid Atoms | |
Solvent Atoms | 161 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |