9F2H | pdb_00009f2h

Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CE0	Chain A

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 o/n with saturated concentration of riluzole 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
2.12	42.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.056	α = 90
b = 43.383	β = 91.44
c = 109.326	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	PIXEL	DECTRIS EIGER2 X CdTe 16M	Toroidal mirror, elliptical beam shape	2021-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.774899	ESRF	ID23-1

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	1.3	46.56	97	0.026	0.999	12.3	5.5		103602			14.431

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	1.3	1.32	89.9		0.363	0.685	1.9	4.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.3	46.56	98450	5140	96.37	0.16856	0.1675	0.1765	0.18898	0.1957	RANDOM	17.108

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]
0.29		0.38	-0.23		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.081
r_dihedral_angle_2_deg	7.485
r_dihedral_angle_1_deg	6.531
r_long_range_B_refined	4.711
r_long_range_B_other	4.384
r_scangle_other	3.069
r_mcangle_it	2.066
r_mcangle_other	2.066
r_scbond_it	1.922
r_scbond_other	1.922
r_angle_refined_deg	1.36
r_mcbond_it	1.296
r_mcbond_other	1.295
r_angle_other_deg	0.478
r_chiral_restr	0.074
r_gen_planes_refined	0.008
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	3488
Nucleic Acid Atoms
Solvent Atoms	628
Heterogen Atoms	34

Software

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