3D2I
Crystal structure of mouse Aurora A (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with 1-{5-[2-(1-methyl-1H-pyrazolo[4,3-d]pyrimidin-7-ylamino)-ethyl]-thiazol-2-yl}-3-(3-trifluoromethyl-phenyl)-urea
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 293 | Protein @ 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 0.1 M bis-Tris propane pH 7.0 and 35% tacsimate; temperature: 293K; cryoprotectant: tacsimate; crystal frozen by immersion in liquid nitrogen. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.92 | α = 90 |
b = 82.92 | β = 90 |
c = 171.964 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 | 160 | IMAGE PLATE | RIGAKU RAXIS IV | 2005-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.54 |
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 | 2.8 | 20 | 97.6 | 0.061 | 7 | 4.8 | 9200 | 8941 |
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) | |||||||||||
2.8 | 2.9 | 99.1 | 0.351 | 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 3D14 | 2.9 | 20 | 8319 | 7469 | 590 | 97.34 | 0.24492 | 0.24065 | 0.29839 | RANDOM | 67.915 |
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] | |
-1.88 | -0.94 | -1.88 | 2.81 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.845 |
r_dihedral_angle_3_deg | 18.742 |
r_dihedral_angle_4_deg | 17.804 |
r_dihedral_angle_1_deg | 4.118 |
r_mcangle_it | 3.097 |
r_scangle_it | 2.366 |
r_mcbond_it | 1.78 |
r_scbond_it | 1.421 |
r_angle_refined_deg | 1.342 |
r_nbtor_refined | 0.297 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2058 |
Nucleic Acid Atoms | |
Solvent Atoms | 35 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
CrystalClear | data reduction |
d*TREK | data scaling |
MOLREP | phasing |