8FE5
Structure of J-PKAc chimera complexed with Aplithianine B
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277.15 | 200 mM Lithium Sulfate, 100 mM HEPES 7.5, 25% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.594 | α = 90 |
b = 171.715 | β = 90.01 |
c = 62.204 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2021-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.51 | 43.59 | 98.26 | 0.026 | 0.999 | 14.75 | 2 | 35478 | 52.23 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.51 | 2.6 | 96.64 | 0.196 | 0.9 | 3.47 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 4WB7 | 2.51 | 43.59 | 1.35 | 35467 | 1999 | 98.28 | 0.1931 | 0.1901 | 0.2432 | 58.08 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 8.1985 |
f_angle_d | 0.9998 |
f_chiral_restr | 0.0528 |
f_bond_d | 0.0089 |
f_plane_restr | 0.0081 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7015 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
PHENIX | refinement |