7P35

Structure of the SARS-CoV-2 3CL protease in complex with rupintrivir

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		SARS-CoV-2 3CL protease

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Triammonium citrate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.023	α = 90
b = 54.024	β = 100.774
c = 114.067	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS 6M		2020-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.256	56.091	84.4	0.998	9.6	2.5		21599

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.256	2.295			0.58

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	SARS-CoV-2 3CL protease	2.256	56.091	21599	1115	84.388	0.203	0.2	0.2581	50.928

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]
0.047		0.022	-0.034		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.343
r_dihedral_angle_4_deg	19.495
r_dihedral_angle_other_3_deg	17.903
r_dihedral_angle_3_deg	16.103
r_lrange_it	9.868
r_lrange_other	9.867
r_dihedral_angle_1_deg	8.117
r_scangle_it	6.215
r_scangle_other	6.214
r_mcangle_it	5.511
r_mcangle_other	5.511
r_scbond_it	4.06
r_scbond_other	4.059
r_mcbond_it	3.643
r_mcbond_other	3.638
r_angle_refined_deg	1.471
r_angle_other_deg	1.222
r_nbd_other	0.212
r_nbd_refined	0.204
r_symmetry_nbd_other	0.195
r_symmetry_nbd_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4694
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing