7NTV

Crystal structure of SARS CoV2 main protease in complex with DN_EG_002 (modelled using PanDDA event map)

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 DN_EG_002 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM DN_EG_002 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
2.61	52.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.941	α = 90
b = 99.743	β = 90
c = 104.126	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	1.00003	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	2.065	49.423	99.82	0.158	0.164	0.044	0.998	11	13.5		44110

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.065	2.119	98.9		1.961	0.54	0.71	1.6	13.75

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	2.065	49.423	44049	2203	99.814	0.196	0.1949	0.2275	RANDOM	42.474

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]
-1.753			2.332		-0.579

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.887
r_dihedral_angle_4_deg	15.226
r_dihedral_angle_3_deg	15.116
r_lrange_it	8.672
r_lrange_other	8.668
r_dihedral_angle_1_deg	7.582
r_scangle_it	6.911
r_scangle_other	6.91
r_mcangle_it	5.07
r_mcangle_other	5.07
r_scbond_it	4.57
r_scbond_other	4.569
r_mcbond_other	3.543
r_mcbond_it	3.54
r_angle_refined_deg	1.633
r_angle_other_deg	1.369
r_nbd_other	0.256
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.2
r_symmetry_nbd_other	0.192
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.153
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4687
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	49

Software

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