3KKV
Structure of PKA with a protein Kinase B-selective inhibitor.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.4 | 294 | Protein stock was at 20mg/ml in 25mM Mes-Bis Tris, pH 6.4, 75mM LiCl, 0.1M EDTA, 1mM DTT. The final concentration of inhibitor in the protein solution was 1mM from a 100mM stock solution of compound dissolved in DMSO.The protein was reacted with inhibitor on ice for 6 hours prior to crystallization.The final concentration of PKI in the protein solution was 2mM from stock 100mM dissolved in water. The final concentration of MEGA8 in the protein solution was 1.5mM from 225mM stock diluted from 790mM in the Hampton additive kit with water. Two microliters of protein were added to 0.35 microliters of 10% glycerol in buffer and put in sitting drops over 15% methanol diluted with water at 4C. Cryo was 100mM MES pH6.4, 100mM LiCl, 25% MeOH, 20% MPD., VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.411 | α = 90 |
b = 75.996 | β = 90 |
c = 80.39 | 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 | CCD | ADSC QUANTUM 210 | 2005-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0000 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 50 | 99.9 | 37 | 41841 | 41799 | 2 | 2 | 24 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.8 | 1.86 | 99.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.8 | 36.206 | 1.9 | 41840 | 41735 | 2108 | 99.88 | 0.2028 | 0.2028 | 0.2017 | 0.2252 | Random |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.079 |
f_angle_d | 0.59 |
f_chiral_restr | 0.034 |
f_plane_restr | 0.002 |
f_bond_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2956 |
Nucleic Acid Atoms | |
Solvent Atoms | 251 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
AMoRE | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |