8PRY

Crystal structure of Trypanosoma cruzi glycerol kinase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	A0A2V2W444

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	20% w/v Polyethylene glycol 3350, 200 mM Magnesium Formate

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.779	α = 117.35
b = 89.321	β = 88.99
c = 97.155	γ = 93.68

Symmetry
Space Group	P 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 PILATUS 2M		2022-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.07	44.61	93.84	0.997	5.6	1.9		117172

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.11			0.518

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.07	44.61	111348	5822	93.84	0.17899	0.17598	0.23753	RANDOM	44.092

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]
-0.26	-0.71	-0.18	-0.6	0.9	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.397
r_dihedral_angle_2_deg	17.627
r_dihedral_angle_1_deg	8.376
r_long_range_B_refined	8.017
r_long_range_B_other	8.011
r_scangle_other	6.451
r_mcangle_it	4.981
r_mcangle_other	4.981
r_scbond_it	4.725
r_scbond_other	4.725
r_mcbond_it	3.672
r_mcbond_other	3.667
r_angle_refined_deg	2.298
r_angle_other_deg	0.776
r_chiral_restr	0.112
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15975
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms

Software

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