2GMX
Selective Aminopyridine-Based C-Jun N-terminal Kinase inhibitors with cellular activity
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2G01 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 277 | Protein was preincubated with the JIP1 peptide at a 5x molar excess. Protein concentration 9-12.6 mg/mL. Hanging drops consisted of 2uL protein plus 2 uL well solution. Well solution:2.8-3.1 M Ammonium Sulfate, 10-14% glycerol. For Co-crystallization experiment with the compound, the compound was dissolved in DMSO at 100 mM concentration. Allow to incubate for at least an hour on ice. Solution was spun for 5 minutes at 2000g prior to setting up for crystallization, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.4 | 72.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.786 | α = 90 |
b = 150.786 | β = 90 |
c = 118.66 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | 110 | CCD | ADSC QUANTUM 210 | 2004-10-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.000 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 3.5 | 20 | 87.7 | 0.078 | 0.078 | 21 | 5.6 | 19198 | 17550 | 1 | 1 | 21.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
3.5 | 3.62 | 99.3 | 0.385 | 0.385 | 4.62 | 5.8 | 1942 |
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 (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2g01 | 3.5 | 19.91 | 2 | 17547 | 16575 | 1658 | 83.3 | 0.278 | 0.278 | 0.266 | 0.351 | RANDOM | 56.4 |
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] | |
-0.54 | 34.46 | -0.54 | 1.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.5 |
c_angle_deg | 1.5 |
c_improper_angle_d | 0.96 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5892 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 74 |
Software
Software | |
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Software Name | Purpose |
CNX | refinement |
ADSC | data collection |
HKL-2000 | data scaling |
CNX | phasing |