8CAC

Crystal structure of SARS-CoV-2 Mpro-H172Y 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	8.5	298	Bis-Tris, Potassium citrate tribasic monohydrate, PEG 3350, Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.032	α = 90
b = 101.709	β = 90
c = 103.205	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 PILATUS 6M-F		2022-06-17	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	2.13	46.061	99.81	0.998	9.71	7.5		40658			42.05

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	2.15	2.23	99.79		0.587	0.94

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	2.13	46.061	40658	2045	99.782	0.215	0.2117	0.2719	52.502

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]
-3.983			5.592		-1.609

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.567
r_dihedral_angle_4_deg	17.25
r_dihedral_angle_3_deg	16.321
r_lrange_other	9.576
r_lrange_it	9.571
r_dihedral_angle_1_deg	7.962
r_scangle_it	6.633
r_scangle_other	6.632
r_mcangle_it	6.154
r_mcangle_other	6.145
r_dihedral_angle_other_3_deg	4.279
r_scbond_it	4.22
r_scbond_other	4.219
r_mcbond_it	3.973
r_mcbond_other	3.962
r_angle_refined_deg	1.504
r_angle_other_deg	1.237
r_symmetry_xyhbond_nbd_refined	0.248
r_nbd_other	0.229
r_nbd_refined	0.203
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.163
r_symmetry_nbd_refined	0.124
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.064
r_symmetry_xyhbond_nbd_other	0.051
r_xyhbond_nbd_other	0.048
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	4666
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	87

Software

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