8C9Q | pdb_00008c9q

Crystal structure of SARS-CoV-2 Mpro-Q189K mutant in complex with 13b-K

X-RAY DIFFRACTION

---

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		298	0.1M PCTP, pH8.0, 25% w/vPEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.671	α = 90
b = 63.897	β = 90.757
c = 103.519	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M-F		2022-08-23	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	1.86	41.99	97.34	0.997	7.89	5		49699			27.45

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	1.86	1.926	94.54		0.778	0.83	5.1

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6y2e	1.86	41.99	49060	2514	97.618	0.221	0.2188	0.23	0.2664	0.27	34.751

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]
-2.096		2.569	-0.208		2.235

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.797
r_dihedral_angle_4_deg	16.75
r_dihedral_angle_3_deg	16.485
r_dihedral_angle_1_deg	7.749
r_lrange_other	6.65
r_lrange_it	6.645
r_scangle_it	4.838
r_scangle_other	4.838
r_dihedral_angle_other_3_deg	4.084
r_mcangle_it	3.69
r_mcangle_other	3.69
r_scbond_it	3.078
r_scbond_other	3.078
r_mcbond_it	2.489
r_mcbond_other	2.483
r_angle_refined_deg	1.529
r_angle_other_deg	1.294
r_symmetry_nbd_refined	0.264
r_nbd_other	0.24
r_nbd_refined	0.198
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.14
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4673
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	86

Software

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