7P3I
Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | 29.9999 %w/v PEG 4K, 0.24 M LiSO4, 0.0999 M TRIS, 0.35 M NaBr |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 59.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 193.67 | α = 90 |
b = 59.564 | β = 106.99 |
c = 81.842 | 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 | 100 | PIXEL | DECTRIS EIGER2 X 16M | 2020-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.999812 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.286 | 92.61 | 97.8 | 0.078 | 0.078 | 10.1 | 4.3 | 39800 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.286 | 2.326 | 97.3 | 1.149 | 1.149 | 1.3 | 4.4 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | none | 2.29 | 92.61 | 37835 | 1962 | 97.78 | 0.2216 | 0.22 | 0.2525 | RANDOM | 74.955 |
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] | |
-2.47 | 0.33 | -2.33 | 3.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.67 |
r_dihedral_angle_4_deg | 14.946 |
r_dihedral_angle_3_deg | 13.494 |
r_dihedral_angle_1_deg | 7.091 |
r_angle_refined_deg | 1.587 |
r_angle_other_deg | 1.289 |
r_chiral_restr | 0.089 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4887 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |