6W4H | pdb_00006w4h

1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R24	PDB entry 3R24

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	5.3 mg/mL 1:1 nsp16/nsp10 in 0.15 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen A7 (0.2 M calcium acetate, 0.1 M HEPES, pH 7.5, 18% w/v PEG 8000), cryoprotectant: 1:1 screen + 50% sucrose

Crystal Properties
Matthews coefficient	Solvent content
4.33	71.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.74	α = 90
b = 167.74	β = 90
c = 51.942	γ = 120

Symmetry
Space Group	P 31 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	C(111)	2020-03-07	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	1.8	30	100	0.06	0.06	0.065	0.024	29.3	7.3		77886		-3	25.4

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	1.8	1.83	100		0.765	0.765	0.828	0.313	0.762	2.6	6.8

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 (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	PDB entry 3R24	1.8	29.76	73752	3821	99.97	0.1497	0.149	0.16	0.1627	0.17	RANDOM	31.531

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]
-0.06	-0.03		-0.06		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.951
r_dihedral_angle_3_deg	8.695
r_dihedral_angle_4_deg	6.592
r_dihedral_angle_1_deg	3.282
r_angle_refined_deg	1.183
r_angle_other_deg	0.321
r_gen_planes_refined	0.055
r_chiral_restr	0.052
r_gen_planes_other	0.051
r_bond_refined_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.951
r_dihedral_angle_3_deg	8.695
r_dihedral_angle_4_deg	6.592
r_dihedral_angle_1_deg	3.282
r_angle_refined_deg	1.183
r_angle_other_deg	0.321
r_gen_planes_refined	0.055
r_chiral_restr	0.052
r_gen_planes_other	0.051
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3201
Nucleic Acid Atoms
Solvent Atoms	486
Heterogen Atoms	65

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.