8QXQ
PsiM in complex with SAH and psilocybin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8PB6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 277 | 100 mM Tris/HCl pH 8.5, 20% PEG 8000, 200 mM MgCl2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.342 | α = 90 |
b = 78.521 | β = 90 |
c = 83.925 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 CdTe 16M | Toroidal mirror | 2023-06-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.7293 | ESRF | ID23-1 |
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 | 0.94 | 15.44 | 99.81 | 0.1082 | 0.1103 | 0.0212 | 0.998 | 13.36 | 26.8 | 211345 | 11.17 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 0.94 | 0.9736 | 99.16 | 4.584 | 4.673 | 0.8985 | 0.383 | 0.53 | 26.9 |
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 | FOURIER SYNTHESIS | FREE R-VALUE | 0.94 | 15.44 | 1.33 | 211060 | 3178 | 99.8 | 0.1367 | 0.1365 | 0.1494 | 16.66 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.2869 |
f_angle_d | 1.3226 |
f_chiral_restr | 0.1065 |
f_plane_restr | 0.018 |
f_bond_d | 0.0133 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2497 |
Nucleic Acid Atoms | |
Solvent Atoms | 451 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHENIX | phasing |