7VIC | pdb_00007vic

The crystal structure of SARS-CoV-2 3C-like protease in complex with a traditional Chinese Medicine Inhibitors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	100 mM MES, pH6, 12% PEG 6000, 0.5% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.178	α = 90
b = 81.411	β = 96.14
c = 91.218	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	CCD	OXFORD ONYX CCD		2021-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION NOVA	1.5406

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	24.499	99.7	0.129	0.991	10.5	4.4		22123

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	2.1	2.18			0.814

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	THROUGHOUT	6LU7	2.1	24.499	22123	1133	99.563	0.217	0.2159	0.22	0.2422	0.25	31.129

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]
0.025		0.001	-0.009		-0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.754
r_dihedral_angle_3_deg	14.662
r_dihedral_angle_4_deg	7.348
r_dihedral_angle_1_deg	6.781
r_lrange_other	4.206
r_lrange_it	4.179
r_angle_other_deg	2.361
r_mcangle_it	2.09
r_mcangle_other	2.089
r_scangle_it	1.664
r_scangle_other	1.663
r_angle_refined_deg	1.22
r_mcbond_it	1.166
r_mcbond_other	1.165
r_scbond_it	0.975
r_scbond_other	0.974
r_symmetry_nbd_other	0.221
r_nbd_refined	0.211
r_nbtor_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.143
r_nbd_other	0.134
r_xyhbond_nbd_refined	0.11
r_symmetry_nbd_refined	0.081
r_symmetry_nbtor_other	0.065
r_chiral_restr	0.048
r_bond_other_d	0.036
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_refined_d	0.002
r_symmetry_xyhbond_nbd_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2295
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing