9M2U | pdb_00009m2u

Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD06

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7K3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289.15	0.1M Bis-Tris pH6.5, 18% (v/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.15	α = 90
b = 52.89	β = 101.799
c = 110.62	γ = 90

Symmetry
Space Group	I 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 PILATUS3 R 200K-A		2024-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	1.967	27.16	98.7	0.13	0.176	0.118	0.987	4.3	3.1		18445

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	1.97	2.02			0.822	1.081	0.695	0.709		3

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	1.967	23.773	18428	942	98.503	0.232	0.228	0.2208	0.3157	0.3015	33.963

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]
-0.918		-0.827	-2.774		3.714

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.092
r_dihedral_angle_3_deg	16.435
r_dihedral_angle_6_deg	14.602
r_lrange_it	10.557
r_lrange_other	10.555
r_scangle_it	9
r_scangle_other	8.998
r_dihedral_angle_1_deg	8.387
r_dihedral_angle_other_2_deg	7.322
r_scbond_it	6.599
r_mcangle_it	6.552
r_mcangle_other	6.55
r_scbond_other	6.487
r_mcbond_other	4.962
r_mcbond_it	4.961
r_angle_refined_deg	2.774
r_angle_other_deg	0.89
r_nbd_refined	0.254
r_symmetry_nbd_other	0.234
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_other	0.226
r_nbtor_refined	0.206
r_symmetry_nbd_refined	0.198
r_xyhbond_nbd_refined	0.188
r_chiral_restr	0.12
r_symmetry_nbtor_other	0.101
r_symmetry_xyhbond_nbd_other	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.015
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2347
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
iMOSFLM	data reduction
PHASER	phasing