5NMH
HLA A02 presenting SLYNTIATL
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.1 M Sodium Cacodylate, pH 6.0, 25% PEG 4000, 0.2 M Ammonium Sulphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.12 | α = 90 |
b = 80.09 | β = 115.75 |
c = 57.58 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2010-04-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.55 | 31.7 | 99.4 | 0.066 | 12.2 | 4.1 | 66024 | 17.2 |
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 | 1.55 | 1.59 | 97.7 | 0.733 | 2.4 | 4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | 1.55 | 31.7 | 62644 | 3346 | 99.39 | 0.16677 | 0.1652 | 0.19587 | RANDOM | 21.371 |
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] | |
-0.43 | -0.3 | -0.5 | 0.84 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.776 |
r_dihedral_angle_4_deg | 18.676 |
r_dihedral_angle_3_deg | 14.674 |
r_dihedral_angle_1_deg | 6.413 |
r_long_range_B_refined | 5.794 |
r_long_range_B_other | 5.566 |
r_scangle_other | 2.039 |
r_angle_refined_deg | 1.886 |
r_mcangle_it | 1.381 |
r_mcangle_other | 1.38 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3153 |
Nucleic Acid Atoms | |
Solvent Atoms | 452 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
xia2 | data reduction |
SCALA | data scaling |
PHASER | phasing |