4QKJ
Glycosylated form of human LLT1, a ligand for NKR-P1, in this structure forming hexamers
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3HUP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.2 | 288 | 40%(v/v) PEG300 and 0.1M citrate phosphate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.06 | α = 90 |
b = 70.06 | β = 90 |
c = 101.71 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 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 | MARMOSAIC 225 mm CCD | Si Mirror, double crystal Si monochromator, Rh mirror | 2011-11-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
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 | 2.7 | 39 | 99.5 | 0.093 | 16.2 | 4.3 | 4431 | 4431 | -3 | 66.1 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.7 | 2.76 | 99.3 | 0.757 | 2 | 4.4 | 273 |
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 (except for the last cycle) | 3HUP | 2.75 | 39 | 4186 | 4186 | 223 | 99.52 | 0.23022 | 0.23022 | 0.22133 | 0.2978 | RANDOM | 40.052 |
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] | |
-0.16 | -0.08 | -0.16 | 0.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.451 |
r_dihedral_angle_3_deg | 21.562 |
r_dihedral_angle_4_deg | 14.554 |
r_long_range_B_refined | 10.195 |
r_long_range_B_other | 10.192 |
r_dihedral_angle_1_deg | 9.828 |
r_mcangle_it | 6.515 |
r_mcangle_other | 6.51 |
r_scangle_other | 6.07 |
r_mcbond_it | 3.959 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 945 |
Nucleic Acid Atoms | |
Solvent Atoms | 15 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
BALBES | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Sawaya | data scaling |