5SLF | pdb_00005slf

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z198195770

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
2.66	53.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.606	α = 90
b = 67.764	β = 90
c = 138.339	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		2022-02-03		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	2.01	138.37	99.9	0.236	0.256	0.097	0.99	6.6	6.8		43194

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	2.01	2.06	98.3		2.851	3.081	1.157	0.358		7	3094

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	2.01	69.17	40957	2068	99.65	0.2038	0.2017	0.21	0.2451	0.26	RANDOM	41.983

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]
-1.31			4.33		-3.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.763
r_dihedral_angle_4_deg	17.342
r_dihedral_angle_3_deg	15.963
r_dihedral_angle_1_deg	8.402
r_mcangle_it	6.142
r_mcbond_it	3.999
r_mcbond_other	3.978
r_angle_refined_deg	1.589
r_angle_other_deg	1.321
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.763
r_dihedral_angle_4_deg	17.342
r_dihedral_angle_3_deg	15.963
r_dihedral_angle_1_deg	8.402
r_mcangle_it	6.142
r_mcbond_it	3.999
r_mcbond_other	3.978
r_angle_refined_deg	1.589
r_angle_other_deg	1.321
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3679
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	41

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.