7Z59 | pdb_00007z59

SARS-CoV-2 main protease (Mpro) covalently modified with a penicillin derivative

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	SARS-CoV-2 Mpro was thawed and diluted to 6 mg/mL (using 20 mM HEPES, pH 7.5, 50 mM NaCl). Beta-Lactam 20e was added to the protein solution to a final concentration of 10 mM; the mixture was incubated for 2 h at ambient temperature prior to dispensing plates. The drop composition was 0.15 uL protein ligand solution, 0.3 uL 11 percent v/v PEG 4000, 0.1 M MES, pH 6.5, and 0.05 ,microL Mpro crystal seed stock. The Mpro crystal seed stock was prepared by crushing Mpro crystals with a pipette tip, suspending them in 30% PEG 4000, 5%v/v DMSO, 0.1 M MES pH 6.5, and vortexing for 60 s with approximately 10 glass beads (1.0 mm diameter, BioSpec products). As reservoir solution was used: 11%v/v PEG 4K, 5%v/v DMSO, 0.1 M MES, pH 6.5. Crystals were grown using the sitting drop vapor diffusion method at 20 degree C and appeared within 24 h, reaching full size within 36 h. Crystals were looped after one week.

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.341	α = 90
b = 53.808	β = 100.649
c = 44.703	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 EIGER X 16M		2021-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	55.695	100	0.188	0.208	0.088	0.997	7.9	10.7		18025

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	100		4.066	4.49	1.893	0.211		10.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6yb7	2	55.695	18017	883	99.978	0.224	0.2223	0.23	0.2516	0.26	48.528

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]
0.378		-0.024	0.305		-0.629

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.145
r_dihedral_angle_3_deg	13.828
r_dihedral_angle_4_deg	10.944
r_dihedral_angle_1_deg	10.656
r_lrange_it	9.864
r_lrange_other	9.863
r_scangle_it	6.118
r_scangle_other	6.117
r_mcangle_other	4.93
r_mcangle_it	4.927
r_scbond_it	4.251
r_scbond_other	4.249
r_mcbond_it	3.345
r_mcbond_other	3.33
r_angle_refined_deg	1.481
r_angle_other_deg	1.37
r_symmetry_nbd_refined	0.258
r_nbd_refined	0.21
r_nbd_other	0.2
r_ext_dist_refined_d	0.193
r_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.169
r_symmetry_xyhbond_nbd_refined	0.149
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.063
r_bond_refined_d	0.008
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	2358
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
BUSTER	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing