6LAM
Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylethanolamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ZFZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.15 | 293.15 | Tris 0.1 M, 2 mM ZnCl2, PEG6000 13% |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 251.879 | α = 90 |
b = 46.729 | β = 90.801 |
c = 84.983 | 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 | 100 | CCD | RAYONIX MX225HE | 2017-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.0 | SPring-8 | BL26B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.79977133822 | 50 | 99.1 | 0.054 | 46.34 | 6.2 | 91433 | 22.09 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.8 | 1.83 | 98 | 0.254 | 5.7 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4zfz | 1.8 | 40.09 | 1.36 | 91416 | 4463 | 98.96 | 0.1932 | 0.1914 | 0.2287 | 29.69 |
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 | 25.0725 |
f_angle_d | 0.9367 |
f_chiral_restr | 0.0551 |
f_bond_d | 0.0074 |
f_plane_restr | 0.0051 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6122 |
Nucleic Acid Atoms | |
Solvent Atoms | 502 |
Heterogen Atoms | 173 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
HKL-2000 | data collection |
MOLREP | phasing |