7NT1 | pdb_00007nt1

Crystal structure of SARS CoV2 main protease in complex with FSP007

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	6.5	293	0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock FSP007 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP007 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.

Crystal Properties
Matthews coefficient	Solvent content
2.68912506	54.2886314

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.175	α = 90
b = 102.171	β = 90
c = 104.38	γ = 90

Symmetry
Space Group	P 21 21 21

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		2020-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000035	SLS	X06SA

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	2.85	46.48	98.9	0.181	0.227	0.135	0.987	6.3	4.6		17362

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	2.85	3			1.12	1.405	0.835	0.478		4.7

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	THROUGHOUT	6lu7	2.85	46.48	17333	874	98.343	0.208	0.2041	0.2047	0.2784	0.2703	56.792

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]
-3.432			7.202		-3.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.141
r_dihedral_angle_3_deg	18.255
r_dihedral_angle_4_deg	15.14
r_lrange_it	9.998
r_lrange_other	9.997
r_dihedral_angle_1_deg	7.698
r_mcangle_it	6.923
r_mcangle_other	6.923
r_scangle_it	6.473
r_scangle_other	6.472
r_mcbond_it	4.28
r_mcbond_other	4.259
r_scbond_it	3.937
r_scbond_other	3.936
r_angle_refined_deg	1.494
r_angle_other_deg	1.197
r_symmetry_xyhbond_nbd_refined	0.3
r_nbd_other	0.214
r_nbd_refined	0.202
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.155
r_ncsr_local_group_1	0.132
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4705
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data processing
Aimless	data scaling
Aimless	data reduction
PHASER	phasing
Coot	model building