6YB7

SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52935% PEG 4000, 5% DMSO, 0.1M MES pH 6.5. 0.15 microlitre protein + 0.3 microlitre reservoir + 0.05 microlitre seed stock
Crystal Properties
Matthews coefficientSolvent content
1.9135.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.429α = 90
b = 52.798β = 103.03
c = 44.611γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91260DiamondI04-1

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
11.2554.7794.20.1040.1090.0310.9999.39.766162
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)
11.251.2757.41.4141.6830.8980.7871.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6LU71.2554.7764937343597.080.14360.14170.1803RANDOM18.206
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]
0.811.17-1.640.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.695
r_dihedral_angle_3_deg11.017
r_dihedral_angle_4_deg9.519
r_dihedral_angle_1_deg7.269
r_angle_other_deg1.412
r_rigid_bond_restr1.387
r_angle_refined_deg1.383
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.695
r_dihedral_angle_3_deg11.017
r_dihedral_angle_4_deg9.519
r_dihedral_angle_1_deg7.269
r_angle_other_deg1.412
r_rigid_bond_restr1.387
r_angle_refined_deg1.383
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2358
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
DIALSdata reduction