6WN4
Structural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich lipid-binding loop in lipoprotein lipase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 16-22% PEG 3350, 250mM Sodium Thiocyanate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.624 | α = 90 |
b = 67.745 | β = 94.369 |
c = 130.073 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | PIXEL | DECTRIS EIGER X 9M | NULL | 2019-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 0.9201 | NSLS-II | 17-ID-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.74 | 29.264 | 99.29 | 0.12 | 0.133 | 0.057 | 0.995 | 10.4 | 5.1 | 23348 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.74 | 2.84 | 93.72 | 0.692 | 0.769 | 0.33 | 0.729 | 1.9 | 5.08 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5D8J | 2.8 | 29.264 | 22291 | 1066 | 99.816 | 0.21 | 0.2079 | 0.2427 | Random selection | 54.434 |
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] | |
1.721 | -2.888 | 2.905 | -4.136 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.766 |
r_dihedral_angle_4_deg | 16.247 |
r_dihedral_angle_3_deg | 15.146 |
r_dihedral_angle_1_deg | 6.917 |
r_lrange_it | 4.519 |
r_lrange_other | 4.519 |
r_mcangle_it | 1.916 |
r_mcangle_other | 1.916 |
r_scangle_it | 1.531 |
r_scangle_other | 1.531 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6797 |
Nucleic Acid Atoms | |
Solvent Atoms | 29 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
HKL-2000 | data scaling |
HKL-2000 | data reduction |
PHASER | phasing |