4Z16
Crystal Structure of the Jak3 Kinase Domain Covalently Bound to N-(3-(((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)pyrimidin-4-yl)amino)methyl)phenyl)acrylamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YVJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.1 M Bis-tris pH 6.5, 16% PEG 3350, 0.2 M ammonium sulfate, 5 mM TCEP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.625 | α = 92.64 |
b = 68.207 | β = 93.06 |
c = 93.13 | γ = 86.2 |
Symmetry | |
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Space Group | P 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 | 100 | CCD | ADSC QUANTUM 315 | 2014-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.97918 | APS | 24-ID-E |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.9 | 92.91 | 97 | 0.13 | 7.1 | 2.2 | 30357 | 64.79 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1YVJ | 2.9 | 92.91 | 30356 | 1495 | 96.98 | 0.204 | 0.2021 | 0.2401 | RANDOM | 65.05 |
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] | |
8.807 | -4.2871 | 4.6577 | -14.5404 | 17.0635 | 5.7334 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 19.2 |
t_omega_torsion | 2.1 |
t_angle_deg | 1 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8711 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms | 144 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |