6Y84

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529315% 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
Matthew coefficientSolvent content
1.9235.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.812α = 90
b = 52.949β = 103.16
c = 44.631γ = 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 I04-10.9126DiamondI04-1

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
11.3954.9397.50.0590.0690.0340.9979.73.65034817.33
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)
11.391.4180.70.9291.1410.650.4812.1

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 REPLACEMENTTHROUGHOUT6LU71.3954.9350331249897.50.1790.17790.2RANDOM21
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]
-3.78090.04220.69783.0831
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.64
t_omega_torsion3.92
t_angle_deg0.98
t_bond_d0.007
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.64
t_omega_torsion3.92
t_angle_deg0.98
t_bond_d0.007
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
t_dihedral_angle_d
t_gen_planes
t_it
t_sum_occupancies
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms16

Software

Software
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
DIALSdata reduction
xia2data reduction
Cootmodel building