7ORE
Crystal structure of JNK3 in complex with light-activated covalent inhibitor MR-II-249 with both non-covalent and covalent binding modes (compound 4)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4X21 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.8 | 277.15 | 16% medium-molecular weight PEG smears (MMW PEG Smears) and 0.1 M HEPES, pH 7.8 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.39 | 48.63 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 52.868 | α = 90 |
b = 71.059 | β = 90 |
c = 107.456 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 PILATUS3 6M | 2018-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97950 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.18 | 29.65 | 99.9 | 0.101 | 0.118 | 0.044 | 0.997 | 10.6 | 7.1 | 21811 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.18 | 2.3 | 99.9 | 0.903 | 1.059 | 0.393 | 0.876 | 2.1 | 7.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4x21 | 2.18 | 29.65 | 20663 | 1096 | 99.84 | 0.2189 | 0.2159 | 0.2759 | RANDOM | 54.154 |
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] | |
4.27 | -1.89 | -2.37 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.506 |
r_dihedral_angle_4_deg | 19.513 |
r_dihedral_angle_1_deg | 18.673 |
r_dihedral_angle_3_deg | 16.293 |
r_angle_refined_deg | 1.274 |
r_angle_other_deg | 1.085 |
r_chiral_restr | 0.046 |
r_gen_planes_refined | 0.008 |
r_bond_refined_d | 0.007 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2837 |
Nucleic Acid Atoms | |
Solvent Atoms | 56 |
Heterogen Atoms | 177 |
Software
Software | |
---|---|
Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |