22EY | pdb_000022ey

Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum SjTGR-WT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A4Z2CZE1-F1	TGR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295.15	4% Tassimate (pH 6.5-8.0) and 15-20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.615	α = 90
b = 86.266	β = 90
c = 182.093	γ = 90

Symmetry
Space Group	P 21 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 S 9M		2024-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.919082	SSRF	BL02U1

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	2.557	91.05	99.9	0.988	6.6	8.3		43384

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	2.557	2.69			0.366

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	2.557	91.047	43204	2157	99.537	0.21	0.2069	0.2083	0.2599	0.2577	50.865

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]
-0.508			1.351		-0.843

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.58
r_dihedral_angle_6_deg	14.379
r_dihedral_angle_2_deg	10.662
r_lrange_it	9.433
r_lrange_other	9.433
r_scangle_it	7.315
r_scangle_other	7.315
r_dihedral_angle_1_deg	7.174
r_mcangle_it	6.645
r_mcangle_other	6.644
r_scbond_it	4.899
r_scbond_other	4.899
r_mcbond_it	4.524
r_mcbond_other	4.523
r_angle_refined_deg	1.656
r_angle_other_deg	0.557
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.22
r_nbd_other	0.208
r_symmetry_nbd_other	0.19
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.168
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_1	0.077
r_chiral_restr	0.074
r_dihedral_angle_other_2_deg	0.024
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9056
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	106

Software

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