9LWZ | pdb_00009lwz

Crystal structure of the oxidized state of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation SjTGR-U597C-oxidized

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

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
2.54	51.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.81	α = 90
b = 86.616	β = 90
c = 182.579	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	295.15	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	0.979183	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	2.07	91.29	100	0.998	11.4	11.7		81335

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	2.19			0.454

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	NONE	2.074	91.29	81189	3903	99.913	0.195	0.1928	0.2022	0.2389	0.2455	43.208

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]
-0.336			-0.237		0.572

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.535
r_dihedral_angle_3_deg	13.719
r_dihedral_angle_2_deg	8.226
r_lrange_other	8.132
r_lrange_it	8.131
r_dihedral_angle_1_deg	7.302
r_scangle_it	6.568
r_scangle_other	6.568
r_mcangle_it	5.129
r_mcangle_other	5.128
r_scbond_it	4.526
r_scbond_other	4.526
r_mcbond_it	3.805
r_mcbond_other	3.803
r_angle_refined_deg	1.698
r_angle_other_deg	0.568
r_nbd_other	0.244
r_symmetry_xyhbond_nbd_other	0.239
r_symmetry_nbd_refined	0.231
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.166
r_dihedral_angle_other_2_deg	0.114
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.077
r_metal_ion_refined	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9048
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	112

Software

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