3V5J
Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with Thienopyrazolylindole Inhibitor 090
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SM2 | pdb entry 1sm2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 294 | 18% PEG3350, 0.1 M Bis-Tris, 0.12 M Li-sulfate, 4% propanol, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.73 | 55.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 146.132 | α = 90 |
b = 69.513 | β = 107.33 |
c = 68.244 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2005-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
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 | 2.5 | 50 | 99 | 0.115 | 7.9 | 3.7 | 22802 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.5 | 2.59 | 98.2 | 0.797 | 3.7 | 2231 |
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 | pdb entry 1sm2 | 2.59 | 38.65 | 20291 | 1039 | 99.01 | 0.2463 | 0.2451 | 0.2699 | RANDOM | 48.706 |
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] | |
10.3198 | -5.8488 | -6.3626 | -3.9571 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 18.15 |
t_omega_torsion | 1.75 |
t_angle_deg | 0.93 |
t_bond_d | 0.007 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3679 |
Nucleic Acid Atoms | |
Solvent Atoms | 54 |
Heterogen Atoms | 74 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
DENZO | data reduction |
PHASER | phasing |
BUSTER | refinement |