9F3A | pdb_00009f3a

Crystal structure of SARS-CoV-2 Mpro in complex with RK-325

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		293	0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH8.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.257	α = 90
b = 62.879	β = 94.083
c = 97.495	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 EIGER X 16M		2023-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	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	2.15	48.62	99.18	0.997	6.3	7		29646

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	2.227			0.559

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.15	48.62	29645	1438	99.197	0.213	0.2101	0.2144	0.2784	0.2827	34.372

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]
-1.921		0.887	1.324		0.466

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.135
r_dihedral_angle_6_deg	14.698
r_dihedral_angle_2_deg	9.477
r_dihedral_angle_1_deg	8.209
r_lrange_other	7.234
r_lrange_it	7.23
r_dihedral_angle_other_3_deg	5.51
r_scangle_it	5.28
r_scangle_other	5.279
r_mcangle_it	4.308
r_mcangle_other	4.308
r_scbond_it	3.372
r_scbond_other	3.371
r_mcbond_it	2.909
r_mcbond_other	2.905
r_dihedral_angle_other_2_deg	2.631
r_angle_refined_deg	1.443
r_angle_other_deg	0.473
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.222
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.19
r_nbd_other	0.171
r_symmetry_xyhbond_nbd_refined	0.171
r_xyhbond_nbd_refined	0.168
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.067
r_chiral_restr	0.062
r_xyhbond_nbd_other	0.046
r_gen_planes_refined	0.007
r_bond_refined_d	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	4691
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	76

Software

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