7NUK | pdb_00007nuk

Crystal structure of SARS CoV2 main protease in complex with EG009 (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 EG009 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM EG009 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
2.6439114	53.506916

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.979	α = 90
b = 100.929	β = 90
c = 104.183	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		2020-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00036	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	2.19	46.29	99.3	0.254	0.264	0.071	0.997	9.6	13.5		37312

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	2.19	2.26	98.7		2.587	0.741	0.699	1.4	13.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6lu7	2.19	46.29	37256	1862	99.088	0.218	0.2155	0.22	0.2608	0.26	RANDOM	38.769

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]
-3.603			5.503		-1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.9
r_dihedral_angle_3_deg	16.7
r_dihedral_angle_4_deg	16.283
r_dihedral_angle_1_deg	7.796
r_lrange_it	7.128
r_lrange_other	7.125
r_scangle_it	5.284
r_scangle_other	5.284
r_mcangle_it	4.26
r_mcangle_other	4.26
r_scbond_it	3.112
r_scbond_other	3.111
r_mcbond_it	2.558
r_mcbond_other	2.554
r_angle_refined_deg	1.54
r_angle_other_deg	1.272
r_nbd_other	0.214
r_symmetry_nbd_refined	0.203
r_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.16
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4725
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	35

Software

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