8A4Y
SARS-CoV-2 non-structural protein-1 (nsp1) in complex with N-(2,3-dihydro-1H-inden-5-yl)acetamide
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE MASSIF-1 |
Synchrotron site | ESRF |
Beamline | MASSIF-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-06-08 |
Detector | DECTRIS PILATUS3 2M |
Wavelength(s) | 0.96546 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 36.688, 36.688, 140.928 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 35.505 - 1.099 |
R-factor | 0.1477 |
Rwork | 0.147 |
R-free | 0.16640 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7k7p |
RMSD bond length | 0.012 |
RMSD bond angle | 1.270 |
Data reduction software | autoPROC (v1.0) |
Data scaling software | autoPROC (v1.0) |
Phasing software | PHENIX (1.19_4092) |
Refinement software | PHENIX (1.19_4092) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 35.505 | 1.120 |
High resolution limit [Å] | 1.099 | 1.100 |
Rmeas | 0.067 | 0.750 |
Rpim | 0.020 | 0.291 |
Number of reflections | 40443 | 1953 |
<I/σ(I)> | 18.4 | 2.3 |
Completeness [%] | 99.9 | 98.1 |
Redundancy | 11.5 | 6.3 |
CC(1/2) | 0.998 | 0.801 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 291.15 | Commercial screen Index 44 (0.1 M HEPES pH 7.5, 25% w/v PEG3350) was chosen for SARS-CoV-2 nsp1 (residues 10 to 126) crystallisation in large quantities using hanging drop method. Frozen stocks of SARS-CoV-2 nsp1 (residues 10 to 126) were thawed on ice and centrifuged in a Thermo Scientific Pico 17 Microcentrifuge, 24-Pl Rotor at 4 degrees, 20000 rpm for 10 min to remove aggregates before the determination of the protein concentration. Subsequently, the protein stock was diluted to 20 mg/mL with precrystallisation buffer (10 mM HEPES and 300 mM NaCl). 400 uL of Index condition 44 was added into each reservoir well. Five protein drops were set on each cover slip by mixing 1 uL of protein solution with 1 uL of the reservoir. The 24-well Linbro plates were incubated at 18 degrees. |