3L6F
Structure of MHC class II molecule HLA-DR1 complexed with phosphopeptide MART-1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1T5W |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 6.5 | 298 | 20% (w/v) PEG 8000 and 0.1 M sodium cacodylate, pH 6.5, EVAPORATION, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.21 | α = 90 |
b = 135.45 | β = 90 |
c = 40.85 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | 100 | CCD | ADSC QUANTUM 315 | 2009-10-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.1 | 43.22 | 100 | 0.074 | 51.3 | 14.2 | 30437 | 30332 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.1 | 2.18 | 100 | 0.46 | 5.2 | 14.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1T5W | 2.1 | 43.22 | 30437 | 30332 | 3039 | 99.7 | 0.2117 | 0.2494 | 0.043 |
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] | |
-1.148 | -7.947 | 9.095 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
angles | 1.58076 |
bonds | 0.009665 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3144 |
Nucleic Acid Atoms | |
Solvent Atoms | 196 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASES | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |