7NT2 | pdb_00007nt2

Crystal structure of SARS CoV2 main protease in complex with FSP006

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 FSP006 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP006 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
2.65545678	53.7090645

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.155	α = 90
b = 100.588	β = 90
c = 104.726	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	2.14	46.45	98.1	0.132	0.149	0.069	0.997	9.8	7.8		39260

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	2.14	2.21			1.329	1.516	0.712	0.634		7.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6lu7	2.145	46.447	39220	1962	97.657	0.204	0.2019	0.21	0.2514	0.25	RANDOM	40.003

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]
-2.693			2.82		-0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35
r_dihedral_angle_4_deg	16.876
r_dihedral_angle_3_deg	15.942
r_dihedral_angle_1_deg	7.942
r_lrange_it	7.812
r_lrange_other	7.783
r_scangle_it	5.54
r_scangle_other	5.539
r_mcangle_it	4.662
r_mcangle_other	4.661
r_scbond_it	3.736
r_scbond_other	3.735
r_mcbond_it	3.109
r_mcbond_other	3.102
r_angle_refined_deg	1.553
r_angle_other_deg	1.291
r_symmetry_nbd_refined	0.245
r_nbd_other	0.219
r_nbd_refined	0.199
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4681
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	61

Software

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