6W75 | pdb_00006w75

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6W4H	PDB entry 6W4H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	292	9.7 mg/mL 1:1 nsp10/nsp16 in 0.5 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), cryoprotectant: 4 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.245	α = 90
b = 166.245	β = 90
c = 98.279	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	2020-03-07	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	1.95	30	100	0.077	0.077	0.083	0.03	25.8	7.6		113483		-3	28.4

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	1.95	1.98	100		0.742	0.742	0.795	0.285	0.88	3.2	7.6

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	FREE R-VALUE	PDB entry 6W4H	1.951	29.925	113455	5610	99.893	0.158	0.1573	0.16	0.1745	0.18	33.856

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]
0.578	0.289		0.578		-1.876

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.895
r_dihedral_angle_3_deg	8.996
r_dihedral_angle_4_deg	7.019
r_lrange_it	6.614
r_lrange_other	6.425
r_dihedral_angle_1_deg	3.157
r_scangle_it	2.853
r_scangle_other	2.853
r_mcangle_it	2.194
r_mcangle_other	2.194
r_scbond_it	1.971
r_scbond_other	1.914
r_mcbond_it	1.31
r_mcbond_other	1.31
r_angle_refined_deg	1.286
r_angle_other_deg	0.329
r_nbd_other	0.234
r_nbd_refined	0.203
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.17
r_symmetry_nbd_refined	0.149
r_metal_ion_refined	0.147
r_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_other	0.118
r_symmetry_nbtor_other	0.095
r_chiral_restr	0.058
r_gen_planes_refined	0.055
r_gen_planes_other	0.051
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6384
Nucleic Acid Atoms
Solvent Atoms	745
Heterogen Atoms	125

Software

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