1AQD
HLA-DR1 (DRA, DRB1 0101) HUMAN CLASS II HISTOCOMPATIBILITY PROTEIN (EXTRACELLULAR DOMAIN) COMPLEXED WITH ENDOGENOUS PEPTIDE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DLH | PDB ENTRY 1DLH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 3.5 | CRYSTALS GREW AS NEEDLES FROM 10MG/ML HLA-DR1 / PEPTIDE COMPLEX, 15% PEG 4000, 100MM GLYCINE, PH 3.5, AT ROOM TEMPERATURE, OVER ONE WEEK. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 56.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 134.514 | α = 90 |
b = 134.32 | β = 104.82 |
c = 131.232 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 98 | IMAGE PLATE | FUJI | 1995-02-14 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE F1 | CHESS | F1 |
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 | 2.45 | 20 | 85 | 0.07 | 14.9 | 2.1 | 73538 | 2 | 37.2 |
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) | |||||||||||
2.45 | 2.57 | 70 | 0.331 | 4.4 | 1.8 |
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 (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1DLH | 2.45 | 6 | 2 | 68842 | 6884 | 89 | 0.216 | 0.216 | 0.21 | 0.279 | 0.26 | RANDOM | 40.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 26 |
x_angle_deg | 2.6 |
x_scangle_it | 0.25 |
x_mcangle_it | 0.2 |
x_scbond_it | 0.2 |
x_mcbond_it | 0.15 |
x_bond_d | 0.016 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11867 |
Nucleic Acid Atoms | |
Solvent Atoms | 152 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | model building |
X-PLOR | refinement |
X-PLOR | phasing |