9R3G | pdb_00009r3g

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum / Plasmodium falciparum chimera COMPLEXED WITH L-LYSINE AND INHIBITOR DDD02174286

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	7.8	293	Protein: 30 mg/ml in 25 mM HEPES, 0.5 M NaCl, 5 % glycerol, 2 mM TCEP, pH 7, 5 mM lysine Reservoir: 25% PEG 3350, 0.2 M Li sulfate, 0.1 M tris pH 7.8

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.808	α = 90
b = 116.579	β = 90
c = 142.991	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 PILATUS 6M		2020-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.9	61.83	100	0.162	0.065	0.998	12.8	13.7		96515

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.949	99.7		1.668	0.662	0.685	2	14

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	1.9	61.83	96445	4822	99.943	0.162	0.16	0.1706	0.1897	0.1978	23.76

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]
-0.292			0.944		-0.652

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.1
r_dihedral_angle_3_deg	12.611
r_dihedral_angle_2_deg	8.669
r_dihedral_angle_1_deg	6.706
r_lrange_it	6.489
r_lrange_other	6.425
r_scangle_other	5.148
r_scangle_it	5.147
r_scbond_it	3.362
r_scbond_other	3.362
r_mcangle_it	3.115
r_mcangle_other	3.115
r_mcbond_it	2.231
r_mcbond_other	2.231
r_angle_refined_deg	1.678
r_dihedral_angle_other_2_deg	0.641
r_angle_other_deg	0.573
r_nbd_refined	0.215
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.181
r_nbd_other	0.172
r_symmetry_nbd_refined	0.147
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.141
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_1	0.07
r_chiral_restr_other	0.026
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8059
Nucleic Acid Atoms
Solvent Atoms	854
Heterogen Atoms	137

Software

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