7R2V | pdb_00007r2v

Structure of nsp14 from SARS-CoV-2 in complex with SAH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QGI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		278	PEG/Imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.176	α = 90
b = 100.312	β = 107.66
c = 90.874	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 2M-F		2022-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.0	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.53	86.6	87.8	0.16	6.8	5		19046

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.532	2.885			0.914

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	7QGI	2.53	20	18062	898	49.35	0.1991	0.1963	0.2031	0.2543	0.2533	RANDOM	57.062

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]
-0.03		0.24	-0.18		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.34
r_dihedral_angle_3_deg	17.096
r_dihedral_angle_4_deg	17.032
r_dihedral_angle_1_deg	6.927
r_angle_refined_deg	1.254
r_angle_other_deg	1.094
r_chiral_restr	0.042
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7064
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	97

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing