9GI6 | pdb_00009gi6

Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of N214A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BB2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.12 M ethylene glycols (Diethylene glycol; Triethylene glycol; Tetraethylene glycol; Pentaethylene glycol); 0.1 M buffer system 3 (Morpheus; 1.0 M Tris (base), BICINE); pH 8.5 and 50% (v/v) Precipitant Mix 1 (Morpheus; 40 % (v/v) PEG 500 MME, 20 % (w/v) PEG 20000)
Crystal Properties
Matthews coefficientSolvent content
2.6152.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.807α = 90
b = 100.574β = 90
c = 102.182γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0322PETRA III, DESYP11

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
11.8355.2894.80.99712.17.54291260.38
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)
11.832.010.943

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.8355.281.3542904201168.860.17560.17390.17410.20740.207736.26
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.6055
f_angle_d0.8542
f_chiral_restr0.0522
f_bond_d0.0072
f_plane_restr0.0066
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4652
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms164

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing