Experiment: 8R14

Structure of compound 11 bound to SARS-CoV-2 main protease

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LVO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10% PEG 4000, 20% glycerol , 0.03 M of each halide (sodium fluoride, sodium bromide, sodium iodide), 0.1 M MES/imidazole pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.79	α = 90
b = 101.23	β = 90
c = 103.79	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2022-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.34	72.47	96.1	0.028	15.4	6.6		136333

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.34	1.42			0.518	0.502	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.336	72.47	136333	6837	84.3	0.1928	0.1904	0.1681	0.2379	0.1968	RANDOM	20.02

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]
11.293			-12.5861		1.2931

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.33
t_omega_torsion	4.9
t_angle_deg	1.23
t_bond_d	0.012
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4691
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	75

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing