4V0I
Water Network Determines Selectivity for a Series of Pyrimidone Indoline Amide PI3KBeta Inhibitors over PI3K-Delta
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WXF | PDB ENTRY 2WXF |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6.5 | 292 | PEG8000 5-10%, ETHYLENE GLYCOL 10-20%, CARBOXYLIC ACIDS 100MM, IN MES-IMIDAZOLE 100MM BUFFER PH 6.5 AT 19C |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.73 | 54.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62 | α = 90 |
b = 216.43 | β = 113.29 |
c = 76.97 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | TOROIDAL MIRROR | 2011-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.54 | 216.43 | 99.4 | 0.07 | 11.8 | 3.3 | 60528 | 2 | 60.4 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.54 | 2.68 | 99.5 | 0.46 | 2.1 | 3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 2WXF | 2.54 | 44.7 | 60472 | 3070 | 98.84 | 0.266 | 0.234 | RANDOM | 56.83 |
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] | |
1.3836 | -4.5431 | -4.1531 | 2.7695 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 20.02 |
t_omega_torsion | 1.8 |
t_angle_deg | 0.95 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 12462 |
Nucleic Acid Atoms | |
Solvent Atoms | 140 |
Heterogen Atoms | 52 |
Software
Software | |
---|---|
Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |