4AGM
Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5086
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04 |
Synchrotron site | Diamond |
Beamline | I04 |
Temperature [K] | 100 |
Detector technology | CCD |
Detector | ADSC CCD |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 64.980, 71.170, 104.960 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 24.620 - 1.520 |
R-factor | 0.1737 |
Rwork | 0.172 |
R-free | 0.19740 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2j1x |
RMSD bond length | 0.006 |
RMSD bond angle | 1.063 |
Phasing software | PHENIX |
Refinement software | PHENIX ((PHENIX.REFINE)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 35.400 | 1.600 |
High resolution limit [Å] | 1.520 | 1.520 |
Rmerge | 0.080 | 0.390 |
Number of reflections | 73697 | |
<I/σ(I)> | 13.8 | 4.1 |
Completeness [%] | 97.8 | 94.2 |
Redundancy | 5.7 | 5.5 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | SITTING-DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE, PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES, PH 7.2, 19% (W/V) POLYETHYLENE GLYCOL 4000, 5 MM DTT. SOAKING BUFFER: 30 MM 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 KCL. |