22FF | pdb_000022ff

Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation in complex with auranofin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.14	α = 90
b = 86.55	β = 90
c = 184.14	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 PILATUS 2M		2023-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.979183	SSRF	BL10U2

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	1.84	50.52	100	0.999	15.7	12.9		117177

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	1.84	1.89			0.645

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	1.84	50.513	117085	5958	99.957	0.192	0.1902	0.1999	0.2243	0.2291	38.832

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]
-0.818			-0.097		0.915

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	16.533
r_dihedral_angle_6_deg	15.116
r_dihedral_angle_3_deg	12.88
r_dihedral_angle_2_deg	7.919
r_lrange_other	7.436
r_lrange_it	7.433
r_dihedral_angle_1_deg	6.723
r_scangle_it	6.23
r_scangle_other	6.23
r_scbond_it	4.479
r_scbond_other	4.478
r_mcangle_it	4.349
r_mcangle_other	4.349
r_mcbond_it	3.481
r_mcbond_other	3.477
r_angle_refined_deg	1.587
r_angle_other_deg	0.548
r_symmetry_xyhbond_nbd_refined	0.244
r_nbd_refined	0.218
r_symmetry_nbd_other	0.189
r_symmetry_nbd_refined	0.185
r_nbd_other	0.177
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.081
r_ncsr_local_group_1	0.072
r_dihedral_angle_other_2_deg	0.02
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9050
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	112

Software

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