6GGF
Structure of the p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9328
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-08-08 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.98 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 65.110, 71.209, 105.351 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.608 - 1.320 |
R-factor | 0.149570400365 |
Rwork | 0.148 |
R-free | 0.17082 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 2j1x |
RMSD bond length | 0.005 |
RMSD bond angle | 0.818 |
Data reduction software | XDS |
Data scaling software | SCALA |
Phasing software | PHENIX |
Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 29.610 | 1.390 |
High resolution limit [Å] | 1.320 | 1.320 |
Rmerge | 0.049 | 0.550 |
Number of reflections | 114821 | |
<I/σ(I)> | 16 | 3.3 |
Completeness [%] | 99.5 | 99.3 |
Redundancy | 5.1 | 4.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm NaCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm NaCl. |