8BHD | pdb_00008bhd

N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (Tbxo4 derivative crystal structure)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Stock protein concentration: 6-9 mg/mL Well solution: 0.1 M HEPES-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 10-20% (vol) glycerol Mix: 400 nL protein solution/seeds + 400 nL well solution Use of microseeding technique to improve crystal size. 1 microliter of a 100 mM Tbxo4 solution (ligand code 7MT) was added to the crystallization drop for a soacking of 1-2 minutes before freezing the crystals.

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.11	α = 90
b = 88.51	β = 105.7
c = 168.64	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	PIXEL	DECTRIS EIGER X 16M	Kirkpatrick-Baez bimorphic mirrors	2020-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.631371	SOLEIL	PROXIMA 1

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	3.17	47.85	99.83	0.1229	0.1259	0.0272	1	14.87	21.2		61436			129

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	3.17	3.283	99.47		2.335	2.395	0.5287	0.789	1.13	19.8

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	SAD	FREE R-VALUE	3.17	47.85	1.34	61359	3073	99.86	0.1942	0.192	0.19	0.2373	0.23	169.93

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	11.8889
f_angle_d	0.5832
f_chiral_restr	0.0473
f_plane_restr	0.0041
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8125
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	71

Software

Software
Software Name	Purpose
PHENIX	refinement
CRANK2	phasing
XSCALE	data scaling
XDS	data reduction
MxCuBE	data collection

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.