3L3G
Crystal structure of HLA-B*4402 in complex with the R5A mutant of a self-peptide derived from DPA*0201
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1M6O | PDB ENTRY 1M6O |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.732 | α = 90 |
b = 81.833 | β = 90 |
c = 110 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2002-08-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
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 | 2.1 | 34 | 96.6 | 0.077 | 5.5 | 2.5 | 27449 | 27449 | 1 | 1 |
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) | |||||||||||
1 | 2.1 | 2.2 | 99.8 | 0.244 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1M6O | 2.1 | 34 | 25432 | 25432 | 1080 | 96.6 | 0.20722 | 0.20722 | 0.2048 | 0.26357 | RANDOM | 28.048 |
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] | |
-0.53 | -0.58 | 1.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.836 |
r_dihedral_angle_4_deg | 16.569 |
r_dihedral_angle_3_deg | 13.971 |
r_dihedral_angle_1_deg | 6.06 |
r_scangle_it | 3.728 |
r_scbond_it | 2.37 |
r_mcangle_it | 1.58 |
r_angle_refined_deg | 1.219 |
r_mcbond_it | 0.849 |
r_chiral_restr | 0.09 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3156 |
Nucleic Acid Atoms | |
Solvent Atoms | 315 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
AMoRE | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |