4WJ5
Structure of HLA-A2 in complex with an altered peptide ligands based on Mart-1 variant epitope
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2X70 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 295 | Good diffracting crystals were obtained by streak seeding |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.18 | α = 90 |
b = 87.14 | β = 90.15 |
c = 79.194 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 PILATUS 2M | 2012-08-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.9789 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.65 | 79.194 | 99.6 | 0.041 | 0.049 | 0.026 | 17 | 3.4 | 102600 | 102600 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.65 | 1.74 | 99.8 | 0.483 | 0.483 | 0.301 | 1.6 | 3.5 | 14976 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | 2X70 | 1.65 | 19.94 | 5093 | 98.76 | 0.1564 | 0.1553 | 0.1787 | RANDOM | 27.234 |
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] | |
-3.89 | -0.73 | 12.12 | -8.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.022 |
r_dihedral_angle_4_deg | 17.902 |
r_dihedral_angle_3_deg | 12.901 |
r_dihedral_angle_1_deg | 6.16 |
r_mcangle_it | 2.685 |
r_mcbond_it | 2.016 |
r_mcbond_other | 2.013 |
r_angle_refined_deg | 1.687 |
r_angle_other_deg | 1.406 |
r_chiral_restr | 0.243 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6308 |
Nucleic Acid Atoms | |
Solvent Atoms | 536 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
XDS | data reduction |
PDB_EXTRACT | data extraction |
AMoRE | phasing |