5NQ3
'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting EFEDLTFLA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5QQ3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | JBS screen, condition A07: 30% MPD, 100 mM Na Citrate, pH 5.6, 200 mM Ammonium Acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.301 | α = 81.48 |
b = 59.696 | β = 67.62 |
c = 66.443 | γ = 68.6 |
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 X 6M | 2016-07-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 1.57 | 61.44 | 96 | 0.06 | 5.7 | 1.9 | 105240 | 23 |
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 | 1.57 | 1.61 | 93.3 | 0.665 | 1.9 |
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 | 5QQ3 | 1.57 | 61.44 | 99669 | 5113 | 95.61 | 0.21989 | 0.21772 | 0.26232 | RANDOM | 26.823 |
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] | |
-0.91 | 0.07 | 0.14 | 0.17 | 0.44 | 0.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.501 |
r_dihedral_angle_4_deg | 18.82 |
r_dihedral_angle_3_deg | 16.436 |
r_dihedral_angle_1_deg | 6.679 |
r_long_range_B_refined | 6.043 |
r_long_range_B_other | 5.885 |
r_scangle_other | 2.267 |
r_angle_refined_deg | 1.818 |
r_mcangle_it | 1.54 |
r_mcangle_other | 1.54 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6290 |
Nucleic Acid Atoms | |
Solvent Atoms | 795 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
xia2 | data reduction |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
PHASER | phasing |