5SLJ | pdb_00005slj

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1430613393

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	278	1.26 M sodium phosphate monobasic, 0.14 M potassium phosphate dibasic

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.183	α = 90
b = 67.638	β = 90
c = 138.562	γ = 90

Symmetry
Space Group	P 21 21 21

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 6M		2022-02-02		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91788	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.3	69.29	100	0.148	0.161	0.062	0.99	7.7	6.5		29254

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	100		0.72	0.781	0.3	0.892		6.7	2826

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	FOURIER SYNTHESIS	THROUGHOUT	7QGI	2.31	69.28	27423	1399	99.95	0.1839	0.1806	0.19	0.2467	0.25	RANDOM	41.933

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]
-1.59			4.72		-3.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.47
r_dihedral_angle_4_deg	20.363
r_dihedral_angle_3_deg	16.229
r_dihedral_angle_1_deg	7.841
r_mcangle_it	6.805
r_mcbond_it	4.452
r_mcbond_other	4.452
r_angle_refined_deg	1.62
r_angle_other_deg	1.327
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.47
r_dihedral_angle_4_deg	20.363
r_dihedral_angle_3_deg	16.229
r_dihedral_angle_1_deg	7.841
r_mcangle_it	6.805
r_mcbond_it	4.452
r_mcbond_other	4.452
r_angle_refined_deg	1.62
r_angle_other_deg	1.327
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3688
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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.