5Z30
The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL41XU |
Synchrotron site | SPring-8 |
Beamline | BL41XU |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2015-06-02 |
Detector | DECTRIS PILATUS3 S 6M |
Wavelength(s) | 1.00000 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 99.399, 108.332, 170.902 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 49.700 - 2.450 |
R-factor | 0.2036 |
Rwork | 0.202 |
R-free | 0.24350 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3wa9 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.080 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHASER (2.5.1) |
Refinement software | PHENIX (1.12_2829) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.530 |
High resolution limit [Å] | 2.440 | 5.250 | 2.440 |
Rmerge | 0.092 | 0.070 | 0.415 |
Rmeas | 0.101 | 0.077 | 0.488 |
Rpim | 0.040 | 0.031 | 0.250 |
Total number of observations | 336465 | ||
Number of reflections | 66632 | 7117 | 6193 |
<I/σ(I)> | 8.2 | ||
Completeness [%] | 97.8 | 99.2 | 92.1 |
Redundancy | 5 | 6.2 | 3 |
CC(1/2) | 0.997 | 0.577 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | potassium cacodylate, potassium chloride, manganese chloride |