7XHY
Crystal structure of MerTK Kinase domain with BMS794833
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 287 | Protein concentration 25 mg/mL Protein storage buffer: Tris-HCl pH 8.0, 500 mM NaCl, 1 mM Tris(2-carboxyethyl)phosphine Hydrochloride (TCEP) Mother Liquor: 0.1 M Tris-HCl pH 8.5, 4.3 M NaCl Protein: Reservoir: Apo-Microseed = 300: 300: 100 nL or 400: 400: 100 nL Co-crystalization 2mM compound preincubation: 2Hours in ICE Cryoprotectant solution: 0.1 M Tris-HCl pH 8.5, 2.5 M NaCl, 20% DMSO, 10 mM compounds |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.127 | α = 90 |
b = 92.533 | β = 90 |
c = 71.435 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 PILATUS 6M | 2021-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 11C | 0.979 | PAL/PLS | 11C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.16 | 50 | 98.5 | 0.081 | 0.088 | 0.034 | 0.985 | 23.2 | 6.8 | 16509 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.16 | 2.2 | 80.5 | 0.478 | 0.528 | 0.218 | 0.931 | 2.1 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
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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 | 7aax | 2.16 | 38.71 | 1.36 | 16477 | 1648 | 98.67 | 0.2125 | 0.208 | 0.2523 | 47.47 |
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 | 21.7364 |
f_angle_d | 1.0447 |
f_chiral_restr | 0.0592 |
f_bond_d | 0.0081 |
f_plane_restr | 0.0066 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2167 |
Nucleic Acid Atoms | |
Solvent Atoms | 40 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHASER | phasing |
HKL-2000 | data scaling |
HKL-2000 | data reduction |
PDB_EXTRACT | data extraction |