9F2I | pdb_00009f2i

Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with 2-amino-1,3-benzothiazol-6-ol

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9F2G	Chains A, B, C, D, E, F, G and H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	PEG 3350 38%, 0.1 M Tris pH 8.5, 50 mM ammonium sulfate and 1 mM InsP6. Protein:precipitant ratio 1:1. Protein concentration: 16.5 mg/ml. Protein buffer: 20 mM Tris pH 8.0 and 150 mM NaCl. Soaking 2 weeks with saturated concentration of riluzole-like compound in PEG 3350 40%, 0.1 M Tris pH 8.5, 50 mM ammonium sulfate, 1 mM InsP6 condition.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.523	α = 90
b = 45.935	β = 93.79
c = 110.012	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 PILATUS3 2M	KB mirror, elliptical beam shape	2021-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.45	109.77	99.8	0.064	0.988	7	4.4		165420			16.766

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47	98.2		0.475	0.618	1.5	3.8

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.45	109.77	157236	8168	99.74	0.18679	0.18536	0.1948	0.21389	0.2203	RANDOM	19.114

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]
-0.01		-0.35	0.58		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.636
r_dihedral_angle_2_deg	6.615
r_dihedral_angle_1_deg	6.356
r_long_range_B_refined	5.13
r_long_range_B_other	4.966
r_scangle_other	3.692
r_mcangle_it	2.417
r_mcangle_other	2.416
r_scbond_it	2.337
r_scbond_other	2.336
r_mcbond_it	1.539
r_mcbond_other	1.539
r_angle_refined_deg	1.424
r_angle_other_deg	0.467
r_chiral_restr	0.07
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6974
Nucleic Acid Atoms
Solvent Atoms	1012
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing
Coot	model building
PDB_EXTRACT	data extraction