8SK4

Co-structure of SARS-CoV-2 (COVID-19 with covalent pyrazoline based inhibitors)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherin-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729810mg/ml Covid-19Mpro (25 mM Hepes pH 7.5, 150 mM NaCl, 1 mM EDTA) was inhibited at 10X molar excess and incubated on ice for 1hr, solution was spun down for 10min at 10,000 rpm. Crystals were grown by hanging-drop vapor diffusion method at 18C. by mixing 1:1, 1:2 and 2:1 ratio of protein to well solution. Crystal grew out of well solution composed of 25% w/v Peg 1500, 100 mM MIB buffer pH 7.0, from PACT screen (Nextal Biotechnologies).
Crystal Properties
Matthews coefficientSolvent content
2.0339.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.51α = 90
b = 53.744β = 101.53
c = 45.594γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2020-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.5418APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
1256.192.20.0780.0840.0310.99915.571708839.19
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.162.11.1121.2420.5420.4425.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT218.7717064890920.19590.19360.2359RANDOM42.22
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]
0.8579-0.7920.6949-1.5528
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.18
t_omega_torsion3.64
t_angle_deg0.95
t_bond_d0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.18
t_omega_torsion3.64
t_angle_deg0.95
t_bond_d0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2310
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms29

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
PHASERphasing