3VYQ
Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SPRING-8 BEAMLINE BL38B1 |
| Synchrotron site | SPring-8 |
| Beamline | BL38B1 |
| Temperature [K] | 95 |
| Detector technology | CCD |
| Collection date | 2007-06-28 |
| Detector | ADSC QUANTUM 315 |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 1 |
| Unit cell lengths | 30.604, 34.093, 61.165 |
| Unit cell angles | 75.28, 77.76, 87.31 |
Refinement procedure
| Resolution | 32.972 - 2.525 |
| R-factor | 0.1954 |
| Rwork | 0.193 |
| R-free | 0.23650 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 3vxv |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.161 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | MOLREP |
| Refinement software | PHENIX ((phenix.refine: 1.6.4_486)) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 2.590 |
| High resolution limit [Å] | 2.500 | 2.500 |
| Rmerge | 0.058 | 0.125 |
| Number of reflections | 7225 | |
| <I/σ(I)> | 16.3 | 5.4 |
| Completeness [%] | 92.8 | 67.4 |
| Redundancy | 2.9 | 1.7 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 293 | 2mM zinc acetate, 100mM sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
