7JPE
Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with m7GpppA Cap-0 and SAM Determined by Fixed-Target Serial Crystallography
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 19-ID |
Synchrotron site | APS |
Beamline | 19-ID |
Temperature [K] | 293 |
Detector technology | PIXEL |
Collection date | 2020-08-02 |
Detector | DECTRIS PILATUS3 X 6M |
Wavelength(s) | 0.97918 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 170.930, 170.930, 52.786 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 49.720 - 2.180 |
R-factor | 0.2179 |
Rwork | 0.217 |
R-free | 0.23700 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6wq3 |
RMSD bond length | 0.005 |
RMSD bond angle | 1.351 |
Data reduction software | DIALS |
Data scaling software | DIALS |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 49.720 | 2.220 |
High resolution limit [Å] | 2.180 | 2.180 |
Number of reflections | 46273 | 2290 |
<I/σ(I)> | 2.55 | 0.53 |
Completeness [%] | 100.0 | 99.7 |
Redundancy | 50.51 | 11.42 |
CC(1/2) | 0.950 | 0.398 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | BATCH MODE | 6.5 | 297 | Protein: 4.0 mg/ml (NSP10/NSP16 1:1), 0.15 M CaCl, 0.01 M Tris-HCl, 2 mM SAM, 1 mM TCEP, 5% Glycerol, pH 7.5. Precipitation buffer: 0.1M MES pH 6.5, 0.9 M NaF. Batch crystallization: 100 ul of protein mixed with 100 ul of precipitation buffer in 500 ul polypropylane tube. Two days before data collection 1 mM EDTA was added to batch crystallization. Crystal were soaked with m7GpppA (0.5 mM) for 10 minutes before data collection. |