7JIB | pdb_00007jib

Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WQ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 4.0 mg/ml (Nsp10/Nsp16 1:1), 0.15 M NaCl, 0.01 M Tris-HCl, 2 mM SAM, 1 mM TCEP, 5% Glycerol, pH 7.5. Precipitation buffer: 0.1 M MES pH 6.5, 0.9 M NaF. Sitting drops made using 0.4 ul of protein mixed with 0.4 ul of precipitation buffer.

Crystal Properties
Matthews coefficient	Solvent content
4.49	72.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.83	α = 90
b = 170.83	β = 90
c = 52.738	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	295	PIXEL	DECTRIS PILATUS3 X 6M		2020-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.65	50	99.6	0.148	0.071	0.981	15	5.2		25799		-3	49.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.7	99.8		1.037	0.507	0.537	1.87	4.9

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 (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	6WQ3	2.65	29.59	24366	1260	98.96	0.1562	0.1549	0.16	0.1809	0.18	RANDOM	55.906

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]
-0.31	-0.15		-0.31		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.658
r_dihedral_angle_3_deg	8.603
r_dihedral_angle_4_deg	8.08
r_dihedral_angle_1_deg	2.042
r_angle_refined_deg	1.291
r_angle_other_deg	0.326
r_gen_planes_refined	0.053
r_chiral_restr	0.052
r_gen_planes_other	0.05
r_bond_refined_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.658
r_dihedral_angle_3_deg	8.603
r_dihedral_angle_4_deg	8.08
r_dihedral_angle_1_deg	2.042
r_angle_refined_deg	1.291
r_angle_other_deg	0.326
r_gen_planes_refined	0.053
r_chiral_restr	0.052
r_gen_planes_other	0.05
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3184
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	193

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	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.