5AY8
Crystal structure of human nucleosome containing H3.Y
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE BL-17A |
Synchrotron site | Photon Factory |
Beamline | BL-17A |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2013-10-26 |
Detector | ADSC QUANTUM 270 |
Wavelength(s) | 0.98 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 101.522, 101.922, 175.736 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.945 - 2.800 |
R-factor | 0.2035 |
Rwork | 0.201 |
R-free | 0.24880 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3av2 |
RMSD bond length | 0.011 |
RMSD bond angle | 1.301 |
Data reduction software | HKL-2000 (705b) |
Data scaling software | HKL-2000 |
Phasing software | PHASER |
Refinement software | PHENIX ((phenix.refine: 1.9_1692)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.900 |
High resolution limit [Å] | 2.800 | 6.030 | 2.800 |
Rmerge | 0.096 | 0.053 | 0.434 |
Rmeas | 0.108 | 0.058 | 0.512 |
Rpim | 0.048 | 0.024 | 0.265 |
Total number of observations | 184460 | ||
Number of reflections | 43676 | ||
<I/σ(I)> | 11 | ||
Completeness [%] | 95.5 | 95.5 | 92.8 |
Redundancy | 4.2 | 5.2 | 3.1 |
CC(1/2) | 0.998 | 0.292 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | sodium acetate, manganese chloride, 2-propanol, trimethylamine N-oxide |