Experiment: 6BYQ

Crystal structure of Tyrosine-tRNA ligase from Helicobacter pylori G27

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H3F	1h3f as per MorDa, TARGET IDENTIFIED WITH SIMBAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	Molecular Dimensions Morpheus screen D11: 10% w/V PEG 4000, 20% V/V glycerol, 0.02 M each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, M 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM Bicine/Tris base pH 8.5: HepyC.00630.a.B1/HepyC.01032.a.B1.PS38283 at 18.5mg/ml: cryo: direct: tray 292683 d11: puck xoe2-4

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.4	α = 90
b = 43.36	β = 121.21
c = 113.7	γ = 90

Symmetry
Space Group	C 1 2 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	RAYONIX MX-300		2017-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.2	40.011	97.1	0.049	0.056	0.999	18.03	4.17		25454			40.13

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	2.2	2.26	84.8		0.498	0.578	0.79	2.6	3.737

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1h3f as per MorDa, TARGET IDENTIFIED WITH SIMBAD	2.2	40.011	1.36	25445	1964	97.33	0.1805	0.1781	0.2091	0.2159	0	60.732

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	2366
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building
SIMBAD	phasing