7U4R
Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((9-propyl-5,6-dihydrothieno[2,3-h]quinazolin-2-yl)thio)butan-2-one, an allosteric inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6MC1 | PDB entry 6MC1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 277 | 100 mM bis-Tris, pH 5.5, 200 mM ammonium acetate, 5% w/v PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.38 | 63.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.376 | α = 90 |
b = 129.505 | β = 91.819 |
c = 83.654 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS EIGER X 16M | 2018-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.9798 | APS | 24-ID-E |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 3.14 | 48.49 | 84.66 | 0.05884 | 0.08216 | 0.996 | 9.07 | 1.7 | 24364 | 89.69 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3.14 | 3.252 | 86.03 | 0.5262 | 0.7351 | 0.586 | 1.62 | 1.7 |
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 | PDB entry 6MC1 | 3.14 | 48.49 | 1.38 | 20634 | 1985 | 84.68 | 0.1774 | 0.1724 | 0.2247 | 95.84 |
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 | 9.675 |
f_angle_d | 0.5242 |
f_chiral_restr | 0.0411 |
f_plane_restr | 0.0037 |
f_bond_d | 0.0031 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7058 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 144 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Coot | model building |
XDS | data scaling |
PHASER | phasing |
XDS | data reduction |