7NT3

Crystal structure of SARS CoV2 main protease in complex with FSCU015

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock FSP006 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSCU015 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.

Crystal Properties
Matthews coefficient	Solvent content
2.65066648	53.6254044

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.005	α = 90
b = 101.348	β = 90
c = 103.982	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 EIGER X 16M		2020-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000031	SLS	X06SA

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.32	49.62	99.8	0.165	0.184	0.081	0.997	9.3	9.3		31612

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)	Redundancy	Number Unique Reflections (All)
1	2.32	2.41			1.748	1.956	0.866	0.606		9.6

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6lu7	2.325	46.302	31556	1626	99.769	0.21	0.2063	0.2709	RANDOM	49.324

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]
-3.228			6.182		-2.954

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.731
r_dihedral_angle_3_deg	17.362
r_dihedral_angle_4_deg	16.127
r_lrange_other	9.088
r_lrange_it	9.084
r_dihedral_angle_1_deg	7.298
r_scangle_it	6.099
r_scangle_other	6.098
r_mcangle_it	5.721
r_mcangle_other	5.712
r_scbond_it	3.774
r_scbond_other	3.773
r_mcbond_it	3.578
r_mcbond_other	3.566
r_dihedral_angle_other_2_deg	1.51
r_angle_refined_deg	1.474
r_angle_other_deg	1.25
r_symmetry_nbd_refined	0.272
r_nbd_other	0.259
r_symmetry_xyhbond_nbd_refined	0.221
r_nbd_refined	0.191
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.149
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.062
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.007
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	4691
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	45

Software

Software
Software Name	Purpose
XDS	data processing
Aimless	data scaling
Aimless	data reduction
PHASER	phasing
REFMAC	refinement
Coot	model building