8P6Q
Racemic structure of TNFR1 cysteine-rich domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 292 | 250 nL of DL-TNFR-1 CRD2 (25 mg/mL) and 250 nL of precipitant (1.5 M Sodium chloride, 10% v/v ethanol, pH 8.5) were mixed in the sitting drop. The single, block shaped crystal was dipped into 2.0 M lithium sulfate and flash frozen in liquid nitrogen during harvesting. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 20.42 | α = 90 |
b = 50.49 | β = 92.94 |
c = 46.21 | 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 EIGER2 XE 16M | 2021-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.6767 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.4 | 34.06 | 100 | 0.999 | 11.3 | 6.01 | 18553 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.4 | 1.42 | 100 | 0.785 | 1 |
Refinement
Statistics | |||||||||||||||||||
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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 | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.4 | 34.06 | 17590 | 943 | 99.98 | 0.20274 | 0.20022 | 0.25144 | 14.739 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.24 | 0.11 | -0.48 | 1.71 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.675 |
r_dihedral_angle_3_deg | 18.454 |
r_dihedral_angle_1_deg | 7.42 |
r_rigid_bond_restr | 4.395 |
r_long_range_B_refined | 3.705 |
r_long_range_B_other | 3.231 |
r_scangle_other | 1.693 |
r_angle_refined_deg | 1.662 |
r_scbond_it | 1.441 |
r_mcangle_it | 1.399 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 738 |
Nucleic Acid Atoms | |
Solvent Atoms | 120 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Coot | model building |