8S0V | pdb_00008s0v

Crystal structure of Cryptosporidium parvum - Trypanosoma cruzi mutant lysyl tRNA synthetase in complex with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ELO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, pH 7, 30 mg/ml Reservoir: 0.2 M Li2SO4, 14-18% PEG3350, 0.1 M tris pH 7.4-7.8

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.136	α = 90
b = 116.697	β = 90
c = 142.882	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	PIXEL	DECTRIS EIGER2 X 16M		2022-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	58.35	99.7	0.082	0.033	0.999	16	13.1		160925			19.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	95		1.212	0.635	0.628	1.6	8.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	58.35	160837	8146	99.697	0.185	0.184	0.1933	0.2083	0.217	22.787

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]
0.063			0.809		-0.872

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.226
r_dihedral_angle_3_deg	12.55
r_dihedral_angle_2_deg	9.752
r_dihedral_angle_1_deg	6.894
r_lrange_it	6.138
r_lrange_other	6.113
r_scangle_it	5.137
r_scangle_other	5.136
r_scbond_it	3.466
r_scbond_other	3.464
r_mcangle_it	2.909
r_mcangle_other	2.909
r_dihedral_angle_other_2_deg	2.469
r_mcbond_it	2.132
r_mcbond_other	2.132
r_angle_refined_deg	1.857
r_angle_other_deg	0.647
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.216
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.179
r_nbd_other	0.153
r_symmetry_xyhbond_nbd_other	0.142
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.107
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8031
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	109

Software

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