22FJ | pdb_000022fj

Crystal structure of the oxidized state of Trx1 from Schistosoma japonicum

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% Tassimate (pH 6.5-8.0) and 15-20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.535	α = 90
b = 90.533	β = 90
c = 150.042	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		2023-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97853	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	2.66	50	95.7	0.97	7.588	3.8		15762

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	2.66	2.71			0.653

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	2.66	43.375	15107	771	91.425	0.224	0.2211	0.2219	0.2845	0.2847	51.385

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]
-0.114			0.467		-0.353

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.255
r_dihedral_angle_6_deg	15.188
r_dihedral_angle_2_deg	13.667
r_lrange_it	13.017
r_lrange_other	13.017
r_scangle_it	8.411
r_scangle_other	8.41
r_mcangle_it	7.435
r_mcangle_other	7.434
r_dihedral_angle_1_deg	6.242
r_scbond_it	5.181
r_scbond_other	5.18
r_mcbond_it	4.764
r_mcbond_other	4.746
r_angle_refined_deg	1.539
r_angle_other_deg	0.522
r_xyhbond_nbd_refined	0.316
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_refined	0.227
r_nbd_other	0.205
r_symmetry_nbd_other	0.204
r_symmetry_nbd_refined	0.184
r_nbtor_refined	0.178
r_ncsr_local_group_3	0.098
r_ncsr_local_group_10	0.096
r_ncsr_local_group_6	0.095
r_ncsr_local_group_8	0.092
r_ncsr_local_group_7	0.086
r_symmetry_nbtor_other	0.083
r_ncsr_local_group_5	0.083
r_ncsr_local_group_9	0.075
r_ncsr_local_group_2	0.074
r_ncsr_local_group_4	0.072
r_ncsr_local_group_1	0.07
r_chiral_restr	0.065
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	4161
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms

Software

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