7NT2

Crystal structure of SARS CoV2 main protease in complex with FSP006


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 FSP006 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP006 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
Crystal Properties
Matthews coefficientSolvent content
2.6554567853.7090645

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.155α = 90
b = 100.588β = 90
c = 104.726γ = 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
12.1446.4598.10.1320.1490.0690.9979.87.839260
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)
12.142.211.3291.5160.7120.6347.9

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6lu72.14546.44739220196297.6570.2040.20190.2514RANDOM40.003
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]
-2.6932.82-0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35
r_dihedral_angle_4_deg16.876
r_dihedral_angle_3_deg15.942
r_dihedral_angle_1_deg7.942
r_lrange_it7.812
r_lrange_other7.783
r_scangle_it5.54
r_scangle_other5.539
r_mcangle_it4.662
r_mcangle_other4.661
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35
r_dihedral_angle_4_deg16.876
r_dihedral_angle_3_deg15.942
r_dihedral_angle_1_deg7.942
r_lrange_it7.812
r_lrange_other7.783
r_scangle_it5.54
r_scangle_other5.539
r_mcangle_it4.662
r_mcangle_other4.661
r_scbond_it3.736
r_scbond_other3.735
r_mcbond_it3.109
r_mcbond_other3.102
r_angle_refined_deg1.553
r_angle_other_deg1.291
r_symmetry_nbd_refined0.245
r_nbd_other0.219
r_nbd_refined0.199
r_symmetry_nbd_other0.189
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.153
r_symmetry_xyhbond_nbd_refined0.141
r_symmetry_nbtor_other0.08
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4681
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms61

Software

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