Experiment: 7NT1

 7NT1

Crystal structure of SARS CoV2 main protease in complex with FSP007


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LU7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock FSP007 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP007 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
Crystal Properties
Matthews coefficientSolvent content
2.6891250654.2886314

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.175α = 90
b = 102.171β = 90
c = 104.38γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000035SLSX06SA

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
12.8546.4898.90.1810.2270.1350.9876.34.617362
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)
12.8531.121.4050.8350.4784.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6lu72.8546.481733387498.3430.2080.20410.278456.792
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]
-3.4327.202-3.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.141
r_dihedral_angle_3_deg18.255
r_dihedral_angle_4_deg15.14
r_lrange_it9.998
r_lrange_other9.997
r_dihedral_angle_1_deg7.698
r_mcangle_it6.923
r_mcangle_other6.923
r_scangle_it6.473
r_scangle_other6.472
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4705
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata processing
Aimlessdata scaling
Aimlessdata reduction
PHASERphasing
Cootmodel building