9EPM

Mpro from SARS-CoV-2 with 4A mutation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CAM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% Polyethylene glycol monomethyl ether 5.000, 200 mM Potassium formate

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.67	α = 90
b = 53.32	β = 101.97
c = 45.2	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS3 6M		2022-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.98	48.125	98.6	0.967	8.87	6.3		18323

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	1.98	2.08			0.346

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.981	48.125	18322	917	98.643	0.201	0.1974	0.2663	52.564

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]
2.504		0.483	-0.793		-1.758

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.522
r_dihedral_angle_3_deg	14.413
r_dihedral_angle_2_deg	11.688
r_lrange_it	9.461
r_lrange_other	9.461
r_dihedral_angle_1_deg	8.247
r_scangle_it	7.655
r_scangle_other	7.653
r_mcangle_it	6.226
r_mcangle_other	6.224
r_scbond_it	5.417
r_scbond_other	5.416
r_mcbond_it	4.636
r_mcbond_other	4.636
r_angle_refined_deg	1.831
r_angle_other_deg	0.706
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.172
r_symmetry_nbd_other	0.16
r_nbd_other	0.116
r_symmetry_nbd_refined	0.105
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_refined	0.06
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2294
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms

Software

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