5NQ1
Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting DFEREGYSL
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QQ3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | PACT screen, condition D02: 0.1M MMT Buffer, pH 5.0, 25% PEG1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.388 | α = 81.24 |
b = 60.288 | β = 67.59 |
c = 65.645 | γ = 67.94 |
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 | DECTRIS PILATUS3 6M | 2016-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.9795 | Diamond | I02 |
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 | 2.14 | 55.87 | 96.9 | 0.128 | 0.172 | 0.115 | 0.979 | 3.4 | 1.9 | 41686 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.14 | 2.2 | 96 | 0.669 | 0.91 | 0.614 | 0.522 | 1.9 | 3024 |
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 | 3QQ3 | 2.14 | 55.87 | 39657 | 2021 | 96.88 | 0.2226 | 0.2195 | 0.283 | RANDOM | 28.043 |
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] | |
-1.74 | -0.23 | -0.32 | 0.01 | 0.29 | 0.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.258 |
r_dihedral_angle_4_deg | 21.301 |
r_dihedral_angle_3_deg | 18.145 |
r_dihedral_angle_1_deg | 7.289 |
r_angle_refined_deg | 1.931 |
r_angle_other_deg | 1.115 |
r_chiral_restr | 0.125 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6294 |
Nucleic Acid Atoms | |
Solvent Atoms | 356 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
DIALS | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
xia2 | data reduction |