3KVX
JNK3 bound to aminopyrimidine inhibitor, SR-3562
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FI3 | PDB entry 3FI3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.5 | 293 | 10MG/ML JNK3 MIXED WITH 1MM AMP-PCP, 2MM MGCL2, 0.4MM ZWITTERGENT 3-14, AND 10% ETHYLENE GLYCOL. CRYSTALS GROWN IN 0.2M NACL, 0.1M BIS-TRIS, 28-31% PEG 3350, PH 5.5. Ligand soaked in to crystals., microbatch, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.362 | α = 90 |
b = 125.642 | β = 90 |
c = 68.744 | 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 | CCD | ADSC QUANTUM 315 | 2007-08-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 1.0 | SSRL | BL9-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.4 | 68.29 | 98.6 | 0.062 | 3.7 | 13329 | 2 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB entry 3FI3 | 2.4 | 23.38 | 13329 | 13142 | 708 | 98.6 | 0.22205 | 0.21957 | 0.26933 | RANDOM | 31.973 |
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] | |
-2.81 | 1.02 | 1.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.783 |
r_dihedral_angle_4_deg | 23.342 |
r_dihedral_angle_3_deg | 17.682 |
r_dihedral_angle_1_deg | 6.884 |
r_scangle_it | 4.788 |
r_scbond_it | 3.347 |
r_mcangle_it | 2.134 |
r_angle_refined_deg | 2.107 |
r_mcbond_it | 1.21 |
r_chiral_restr | 0.127 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2531 |
Nucleic Acid Atoms | |
Solvent Atoms | 27 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |