6Z9V
Human Class I Major Histocompatibility Complex, A02 allele, presenting IIGWMWIPV
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5EUL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | PACT premier screen, condition G06: 0.2M Na Formate, 0.1M Bis-Tris Propane, 20% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.19 | α = 90 |
b = 85.19 | β = 90 |
c = 232.55 | γ = 120 |
Symmetry | |
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Space Group | P 32 1 2 |
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 | DECTRIS PILATUS3 6M | 2017-10-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97622 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.01 | 73.78 | 100 | 0.142 | 0.149 | 0.044 | 0.999 | 13.4 | 11.2 | 64808 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.01 | 2.06 | 100 | 1.755 | 1.838 | 0.541 | 0.605 | 11.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 5EUL | 2.01 | 73.78 | 61437 | 3287 | 99.99 | 0.1778 | 0.1758 | 0.2164 | RANDOM | 35.743 |
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] | |
-0.84 | -0.42 | -0.84 | 2.72 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.084 |
r_dihedral_angle_4_deg | 17.904 |
r_dihedral_angle_3_deg | 15.943 |
r_dihedral_angle_1_deg | 7.167 |
r_angle_refined_deg | 1.794 |
r_angle_other_deg | 1.39 |
r_chiral_restr | 0.084 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6340 |
Nucleic Acid Atoms | |
Solvent Atoms | 491 |
Heterogen Atoms | 145 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |