6WKQ | pdb_00006wkq

1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer from SARS-CoV-2 in Complex with Sinefungin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6W75	PDB entry 6W75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	5.3 mg/mL 1:1 nsp10/nsp16 in 0.15 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen F10 (0.4 M potassium/sodium tartrate), soak and cryoprotection: 5 mM SFG, 4 M sodium formate, 3 hrs

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.247	α = 90
b = 166.247	β = 90
c = 98.139	γ = 120

Symmetry
Space Group	P 32 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	MARMOSAIC 300 mm CCD	BE	2020-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.98	30	100	0.071	0.071	0.078	0.033	22.2	5.5		108598		-3	31.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.01	100		0.784	0.784	0.874	0.384	0.724	2	5.2

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	PDB entry 6W75	1.98	29.922	108429	5357	99.96	0.163	0.1623	0.17	0.1799	0.19	38.118

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]
0.283	0.141		0.283		-0.917

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.641
r_dihedral_angle_3_deg	8.057
r_lrange_it	6.904
r_lrange_other	6.735
r_dihedral_angle_4_deg	5.649
r_scangle_it	3.46
r_scangle_other	3.46
r_mcangle_it	2.656
r_mcangle_other	2.655
r_dihedral_angle_1_deg	2.463
r_scbond_it	2.34
r_scbond_other	2.327
r_mcbond_it	1.603
r_mcbond_other	1.603
r_dihedral_angle_other_3_deg	1.44
r_angle_refined_deg	1.342
r_angle_other_deg	0.347
r_nbd_other	0.223
r_nbd_refined	0.2
r_symmetry_xyhbond_nbd_refined	0.177
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.171
r_symmetry_nbd_refined	0.137
r_xyhbond_nbd_refined	0.121
r_metal_ion_refined	0.121
r_symmetry_nbtor_other	0.096
r_chiral_restr	0.06
r_gen_planes_refined	0.055
r_gen_planes_other	0.051
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6408
Nucleic Acid Atoms
Solvent Atoms	636
Heterogen Atoms	107

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing