6YJB
VcaM4I restriction endonuclease 5hmC-ssDNA complex
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | EMBL/DESY, HAMBURG BEAMLINE X13 |
Synchrotron site | EMBL/DESY, HAMBURG |
Beamline | X13 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-11-28 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1.0064 |
Spacegroup name | P 62 2 2 |
Unit cell lengths | 128.685, 128.685, 110.895 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 29.770 - 1.550 |
R-factor | 0.1436 |
Rwork | 0.142 |
R-free | 0.16360 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6yex |
RMSD bond length | 0.008 |
RMSD bond angle | 1.358 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 29.770 | 1.640 |
High resolution limit [Å] | 1.550 | 1.550 |
Rmeas | 0.103 | 2.364 |
Number of reflections | 78576 | 12449 |
<I/σ(I)> | 26.96 | 1.96 |
Completeness [%] | 99.9 | 99.7 |
Redundancy | 39.2 | 39.9 |
CC(1/2) | 1.000 | 0.752 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291 | Reservoir solution: 1.6 M (NH4)2SO4, 0.1 M MES pH 5.25; protein:DNA solution: 300 mM NaCl, 15 mM Tris-HCl pH 8.5 and 1mM TCEP. For cryo-protection the reservoir solution was diluted with glycerol to achieve 30% concentration. 0.1 M spermine tetrahydrochloride was used as an additive. |