9LWM | pdb_00009lwm

Crystal structure of reduced state of the 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

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
2.68	54.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.44	α = 90
b = 88.16	β = 90
c = 185.516	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 6M		2024-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.979460	SSRF	BL19U1

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	2.02	50.626	99.9	0.999	14.3	12.9		91695

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	2.03	2.15			0.472

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	2.026	50.626	91689	4585	99.886	0.203	0.2012	0.2092	0.2459	0.2526	44.972

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]
0.324			-1.057		0.733

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.739
r_dihedral_angle_3_deg	13.363
r_lrange_other	8.295
r_lrange_it	8.294
r_dihedral_angle_2_deg	7.469
r_dihedral_angle_1_deg	6.548
r_scangle_it	6.297
r_scangle_other	6.297
r_mcangle_it	4.896
r_mcangle_other	4.896
r_scbond_it	4.131
r_scbond_other	4.13
r_mcbond_it	3.529
r_mcbond_other	3.529
r_angle_refined_deg	1.555
r_angle_other_deg	0.53
r_symmetry_nbd_refined	0.213
r_nbd_refined	0.208
r_nbd_other	0.206
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.081
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.072
r_ncsr_local_group_1	0.065
r_dihedral_angle_other_2_deg	0.023
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	333
Heterogen Atoms	107

Software

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