6OD8 | pdb_00006od8

Crystal structure of a putative aspartyl-tRNA synthetase from Leishmania major Friedlin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Microlytic MCSG-1 screen G9: 20% (w/V) PEG 3350, 200mM sodium formate: LemaA.00612.a.B1.PW38547 at 21.8mg/ml: cryo: 20% EG in two steps: tray 306454 G9: puck xyn7-2. For experimental phasing, a crystal from the same well was incubated for 10sec each in a solution of a) 90% reservoir and 10% 2.5M Sodium iodide in ethylene glycol and a solution of b) a) 80% reservoir and 20% 2.5M Sodium iodide in ethylene glycol a s and vitrified: puck: bbh6-4. Well diffracting monoclinic crystals with a larger unit cell and four copies of the protein in the ASU also grew under condition MCSG-1 D9: 25% (w/V) PEG 3350, 200mM NaCl, 100mM Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.01	α = 90
b = 142.36	β = 97.2
c = 68.28	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	CCD	RIGAKU SATURN 944+		2019-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.85	46.111	99	0.061	0.064	0.999	20.88	8.76		97249			29.613

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	92.1		0.334	0.4	0.872	2.87	3.109

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.85	46.111	1.36	97236	1892	99.01	0.1574	0.1567	0.16	0.1919	0.19	0	29.6474

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7927
Nucleic Acid Atoms
Solvent Atoms	820
Heterogen Atoms	77

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building
ARP/wARP	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.