7MLK
Crystal structure of human PI3Ka (p110a subunit) with MMV085400 bound to the active site determined at 2.9 angstroms resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4TUU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 286 | 8% (w/v) PEG 6000, 0.1 M CHES pH 9.75, 0.64 M Sodium Formate and AMP, 5 mM TCEP pH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.849 | α = 90 |
b = 134.794 | β = 90 |
c = 141.95 | 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 | 95.15 | PIXEL | DECTRIS PILATUS 6M | 2015-04-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.91 | 141.95 | 99.6 | 0.069 | 0.075 | 0.03 | 0.999 | 15.9 | 6.5 | 25366 | 106.31 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.913 | 2.923 | 100 | 0.975 | 1.062 | 0.414 | 0.789 | 6.3 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 4TUU | 2.91 | 97.75 | 25315 | 1281 | 99.1 | 0.2074 | 0.2054 | 0.2422 | RANDOM | 105.29 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
21.76 | 19.0124 | -40.7724 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.692 |
c_mcangle_it | 2.449 |
c_scbond_it | 1.631 |
c_mcbond_it | 1.367 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7235 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
BUSTER | phasing |
BUSTER | refinement |
PDB_EXTRACT | data extraction |