Experiment: 8U2P

Crystal Structure of Glycine--tRNA ligase from Mycobacterium tuberculosis (G5A bound)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8T5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Morpheus A2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. MytuD.19107.a.UW1.PS38711 at 24.9 mg/mL. Crystals grown in a clover Jr. plate using conditions for PDB entry 8T5N. 4 hour soak in 5mM G5A in crystallant. Plate SS-Clover book 3, pg35. Puck: PSL-1308, Cryo: direct.

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.293	α = 90
b = 124.293	β = 90
c = 131.383	γ = 120

Symmetry
Space Group	P 61 2 2

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 EIGER2 XE 9M		2023-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9795	NSLS-II	19-ID

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	2.25	49.8	100	0.198	0.201	0.036	0.999	18.1	30.7		29045

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	2.25	2.32		100	2.394	2.434	0.439	0.718		30.4

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.25	45.15	1.35	28975	1464	99.92	0.18	0.1786	0.1929	0.2078	0.2172

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	14.574
f_angle_d	0.593
f_chiral_restr	0.042
f_plane_restr	0.006
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3213
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	64

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing