7LCZ
Crystal structure of the ARM domain from Drosophila SARM1 in complex with NMN
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.1 M SPG buffer (pH 8.0) and 25% PEG1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.921 | α = 103.516 |
b = 50.788 | β = 101.899 |
c = 76.054 | γ = 95.261 |
Symmetry | |
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Space Group | P 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 16M | 2019-05-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.95372 | Australian Synchrotron | MX2 |
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 | 1.46 | 71.88 | 83.5 | 0.999 | 15.9 | 7.1 | 83026 | 19.54 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.46 | 1.6 | 0.633 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MIRAS | FREE R-VALUE | 1.65 | 37.67 | 1.96 | 57342 | 3551 | 86.5 | 0.2125 | 0.212 | 0.2295 | 27.77 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.2683 |
f_angle_d | 0.4732 |
f_chiral_restr | 0.0322 |
f_plane_restr | 0.0034 |
f_bond_d | 0.0025 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4724 |
Nucleic Acid Atoms | |
Solvent Atoms | 596 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
autoSHARP | phasing |
Coot | model building |
BUCCANEER | model building |
XDS | data reduction |
Aimless | data scaling |