2Q6W
The structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet integrin peptide associated with fetal and neonatal alloimmune thrombocytopenia
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.4 | 297 | 10-20% PEG 8000, 0.1M sodium acetate, 10% (v/v) glycerol, 0.01M Cd2+, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.96 | 58.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.169 | α = 90 |
b = 92.169 | β = 90 |
c = 248.555 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | 98 | CCD | ADSC QUANTUM 4 | 2002-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.1 | NSLS | X25 |
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 | 2.25 | 30 | 94 | 0.12 | 15.8 | 51116 | 48049 | 2 | 2 | 42.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.25 | 2.308 | 55.7 | 0.36 | 3.04 |
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 (All) | 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 | PDB entry 1DLH | 2.25 | 20.05 | 2 | 47777 | 44561 | 3684 | 93.27 | 0.214 | 0.20984 | 0.26543 | RANDOM | 42.241 |
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] | |
0.82 | 0.82 | -1.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.671 |
r_dihedral_angle_4_deg | 22.268 |
r_dihedral_angle_3_deg | 18.375 |
r_dihedral_angle_1_deg | 8.266 |
r_scangle_it | 5.641 |
r_scbond_it | 3.834 |
r_mcangle_it | 2.551 |
r_angle_refined_deg | 2.478 |
r_mcbond_it | 1.677 |
r_nbtor_refined | 0.34 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6043 |
Nucleic Acid Atoms | |
Solvent Atoms | 487 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |