7DDC | pdb_00007ddc

Crystal structure of SARS-CoV-2 main protease in complex with Tafenoquine

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, SITTING DROP		293	0.1 M Ammonium acetate,0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10000

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.294	α = 90
b = 54.675	β = 100.861
c = 44.79	γ = 90

Symmetry
Space Group	C 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	RAYONIX MX300HE		2020-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.175	27.586	99.62	0.047	27.382	3.7		14115

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.175	2.253			0.234		3.7

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	6LU7	2.175	27.586	14115	708	99.626	0.184	0.1812	0.19	0.2338	0.24	30.516

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]
-0.028		-0.304	-0.032		0.165

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.056
r_dihedral_angle_3_deg	15.514
r_dihedral_angle_4_deg	15.186
r_lrange_it	8.281
r_dihedral_angle_1_deg	7.933
r_lrange_other	7.374
r_scangle_it	5.412
r_scangle_other	4.923
r_mcangle_it	3.666
r_mcangle_other	3.665
r_scbond_it	3.562
r_scbond_other	3.281
r_mcbond_it	2.454
r_mcbond_other	2.451
r_angle_refined_deg	1.38
r_angle_other_deg	1.333
r_symmetry_xyhbond_nbd_refined	0.304
r_nbd_other	0.277
r_nbd_refined	0.23
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.155
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2329
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing