9GIL | pdb_00009gil

Crystal structure of SARS-CoV-2 Mpro with compound 12

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		proprietary model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	(NH4)2SO4: 1.6 M ; Dioxane: 10 %v/v ; MES: 0.1 M pH: 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.605	α = 90
b = 106.61	β = 103.043
c = 55.375	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 EIGER2 X 16M		2023-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9537	SLS	X10SA

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	1.721	53.946	88.2	0.1393	0.1542	0.0652	0.985	5.24	4.98		43129

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)
	1.721	1.846	52.7		0.94	1.0352	0.4297	0.673	1.38	5.51	2156

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	1.849	53.946	42493	2155	90.632	0.194	0.192	0.1987	0.2363	0.2449	23.047

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]
-0.386		0.321	-0.667		0.816

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	34.679
r_dihedral_angle_2_deg	34.014
r_dihedral_angle_4_deg	14.538
r_dihedral_angle_3_deg	12.4
r_dihedral_angle_6_deg	12.271
r_dihedral_angle_1_deg	7.075
r_lrange_it	4.112
r_lrange_other	3.964
r_mcangle_it	1.817
r_mcangle_other	1.817
r_scangle_it	1.778
r_scangle_other	1.778
r_angle_refined_deg	1.37
r_angle_other_deg	1.166
r_scbond_it	1.096
r_scbond_other	1.096
r_mcbond_it	1.062
r_mcbond_other	1.057
r_symmetry_xyhbond_nbd_refined	0.17
r_nbd_refined	0.161
r_nbtor_refined	0.151
r_symmetry_nbd_other	0.149
r_xyhbond_nbd_refined	0.133
r_symmetry_nbd_refined	0.126
r_nbd_other	0.118
r_symmetry_nbtor_other	0.068
r_chiral_restr	0.06
r_ncsr_local_group_1	0.033
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4734
Nucleic Acid Atoms
Solvent Atoms	455
Heterogen Atoms	145

Software

Software
Software Name	Purpose
autoPROC	data processing
autoPROC	data processing
Aimless	data scaling
autoPROC	data processing
REFMAC	refinement
autoPROC	data reduction
PHASER	phasing