7PNS
Protein kinase A catalytic subunit in complex with PKI5-24 and EN081
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5M6Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277.15 | Protein at 8 mg/mL in 100 mM Mes-Bis-Tris pH 6.9, 75 mM Lithium chloride, 1 mM DTT, 100 mM Sodium-EDTA. Master-Mix: 540 uL of protein + 15 uL 10 mM Mega8 in Water + 45 uL 10 mM PKI5-24 in protein-buffer. 70 % Master-Mix mixed with 30 % 50 mM ligand in DMSO before setting of drops. 15-24 % Methanol/Water in Reservoir. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.444 | α = 90 |
b = 73.122 | β = 90 |
c = 77.172 | 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 | PIXEL | DECTRIS EIGER2 X 16M | 2021-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.033193 | PETRA III, DESY | P11 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | CC (Half) | 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 | 1.855 | 42.171162889 | 97 | 0.054 | 0.999 | 28.79 | 13.31 | 33232 | 32.4678264541 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.855 | 1.96 | 96.1 | 0.5 | 0.962 | 5.88 | 13.58 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5M6Y | 1.855 | 42.171162889 | 1.37197285521 | 33232 | 1662 | 97.0277372263 | 0.17557903644 | 0.174237982654 | 0.201529813393 | 42.5461014425 |
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 | 16.908294546 |
f_angle_d | 1.00563999118 |
f_chiral_restr | 0.0592135535102 |
f_bond_d | 0.010402418069 |
f_plane_restr | 0.00675642988432 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2805 |
Nucleic Acid Atoms | |
Solvent Atoms | 151 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |