5F5W | pdb_00005f5w

Crystal structure of the alpha subunit of glycyl tRNA synthetase (GlyRS) from Aquifex aeolicus in complex with an analog of glycyl adenylate (Gly-SA)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J5W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	Drops containing 1 microliter of alpha-AaGlyRS at 15 mg/ml yielded crystals at 18C when mixed with 1 microliter of a reservoir solution containing 30% polyethylene glycol monomethyl ether 2000 and 100 mM potassium thiocyanate. Crystals were soaked for 2 days in a solution containing a final concentration of 28 mM GSAd by mixing 1.3 microliters of the drop containing crystals, 2.5 microliters of reservoir solution and 1.5 microliters of GSAd at 100 mM

Crystal Properties
Matthews coefficient	Solvent content
2.72	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.829	α = 90
b = 130.01	β = 90
c = 145.52	γ = 90

Symmetry
Space Group	P 2 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	CCD	MARMOSAIC 300 mm CCD		2015-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9785	APS	21-ID-G

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	2.81	83.43	100	0.084	9.7	4.4	47824	47824			55

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	2.81	2.91	100		0.584	2.2	4.5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1J5W	2.81	80.166	1.34	47741	2409	99.92	0.2396	0.2389	0.24	0.2521	0.25	random selection

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	16.336
f_angle_d	1.462
f_chiral_restr	0.098
f_bond_d	0.011
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11740
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	135

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
MOSFLM	data reduction
BALBES	phasing
Coot	model building

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.