7WRS | pdb_00007wrs

Crystal structure of the chicken isoleucyl-tRNA synthetase 1 (IARS1) UNE-I complexed with glutamyl-tRNA synthetase 1 (EARS1)

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R3Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	0.84 M NaH2PO4, 1.76 M K2HPO4, and 0.1 M sodium acetate, pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.02	α = 90
b = 155.55	β = 90
c = 44.22	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	RAYONIX MX225-HS		2019-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	PAL-XFEL BEAMLINE NCI	1.2782	PAL-XFEL	NCI

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	fixed target	fixed target

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	20 (fs)			9.7 (KeV)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (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	2.4	77.8	100	0.995	0.1438	5.2	622.9		39660			50.62

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44			0.649

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4R3Z	2.4	71.51	1.34	39632	1987	99.92	0.194	0.1914	0.19	0.2437	0.24	57.59

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.2569
f_angle_d	0.978
f_chiral_restr	0.0565
f_bond_d	0.009
f_plane_restr	0.0061

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6358
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	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.