6YKF
VcaM4I restriction endonuclease in the presence of 5mC-modified ssDNA
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P13 (MX1) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-12-15 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.97626 |
Spacegroup name | P 62 2 2 |
Unit cell lengths | 129.000, 129.000, 110.911 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 42.230 - 1.480 |
R-factor | 0.1702 |
Rwork | 0.169 |
R-free | 0.18810 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6yjb |
RMSD bond length | 0.006 |
RMSD bond angle | 1.288 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 42.230 | 1.560 |
High resolution limit [Å] | 1.480 | 1.480 |
Rmeas | 0.096 | 1.019 |
Number of reflections | 90208 | 14319 |
<I/σ(I)> | 14.95 | 1.91 |
Completeness [%] | 98.9 | 98.5 |
Redundancy | 10.6 | 10.1 |
CC(1/2) | 0.999 | 0.742 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.25 | 291 | RESERVOIR SOLUTION: 1.6 M (NH4)2SO4 , 0.1 M MES PH 5.25; PROTEIN:DNA SOLUTION: 0.3 M NACL, 15 MM TRIS-HCL PH 8.5 AND 1 MM TCEP. FOR CRYO-PROTECTION THE RESERVOIR SOLUTION WAS DILUTED WITH GLYCEROL TO ACHIEVE 30% CONCENTRATION. |