8A55

Structure of N-terminal SARS-CoV-2 nonstructural protein 1 (nsp1) at atomic resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7K7P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291.15Commercial 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.
Crystal Properties
Matthews coefficientSolvent content
1.8232.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.81α = 90
b = 36.81β = 90
c = 140.96γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-09-24MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.82656ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
10.9932.6399.490.99812.737.755025
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.991.02598.390.2670.837.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7K7P0.9932.631.3455001275299.50.15440.15340.173424.5782
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms909
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
XDSdata reduction