4KS8
PAK6 kinase domain in complex with sunitinib
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4KS7 | PDB entry 4KS7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | 30% (v/v) isopropanol, 0.1M MES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.616 | α = 90 |
b = 60.099 | β = 90 |
c = 99.979 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 100 | CCD | ADSC QUANTUM 270 | mirrors | 2012-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 1.0000 | NSLS | X6A |
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 | 1.95 | 50 | 100 | 0.117 | 17.47 | 6.8 | 22562 | 20 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.95 | 2.02 | 100 | 0.885 | 2 | 6.7 | 2187 |
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 4KS7 | 1.95 | 38.46 | 21308 | 1149 | 99.38 | 0.22026 | 0.21813 | 0.26099 | RANDOM | 28.004 |
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] | |
0.63 | 1.04 | -1.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.502 |
r_dihedral_angle_4_deg | 17.471 |
r_dihedral_angle_3_deg | 13.235 |
r_dihedral_angle_1_deg | 5.675 |
r_angle_refined_deg | 1.337 |
r_angle_other_deg | 0.708 |
r_chiral_restr | 0.067 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2293 |
Nucleic Acid Atoms | |
Solvent Atoms | 171 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |