8C9O

Crystal structure of SARS-CoV-2 Mpro-S144A mutant in complex with 13b-K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Ethylene glycols, HEPES, PEG 500 MME, PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.766	α = 90
b = 99.689	β = 90
c = 103.307	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	293	PIXEL	DECTRIS PILATUS 6M-F		2022-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.003	PETRA III, DESY	P11

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	1.69	49.31	99.88	0.999	13.71	13.4		78872			31.02

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	99.7		3.38	0.426

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	6y2e	1.69	49.31	78872	3819	99.853	0.2	0.1984	0.2344	38.737

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]
-1.874			2.545		-0.671

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.55
r_dihedral_angle_4_deg	16.321
r_dihedral_angle_3_deg	15.29
r_lrange_it	7.883
r_lrange_other	7.874
r_dihedral_angle_1_deg	7.788
r_scangle_it	5.996
r_scangle_other	5.995
r_mcangle_it	4.825
r_mcangle_other	4.825
r_scbond_it	4.06
r_scbond_other	4.06
r_dihedral_angle_other_3_deg	3.715
r_mcbond_it	3.462
r_mcbond_other	3.46
r_angle_refined_deg	1.654
r_angle_other_deg	1.378
r_nbd_refined	0.204
r_symmetry_xyhbond_nbd_refined	0.185
r_symmetry_nbd_other	0.182
r_nbd_other	0.177
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.126
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.025
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4705
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHENIX	phasing