22FG | pdb_000022fg

Crystal structure of the oxidized state of TRP14 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		289.15	0.2 M lithium sulfate monohydrate, 0.1 M HEPES (pH 5.5), and 25% polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.631	α = 90
b = 54.833	β = 90
c = 37.751	γ = 90

Symmetry
Space Group	P 21 21 2

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	1.69	37.97	100	0.999	15.3	11.5		12749

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	1.69	1.73			0.484

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	1.692	37.97	12719	589	99.953	0.203	0.2017	0.207	0.2423	0.2482	28.948

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]
0.996			-0.112		-0.885

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.921
r_dihedral_angle_6_deg	12.827
r_dihedral_angle_2_deg	7.837
r_dihedral_angle_1_deg	6.37
r_lrange_it	6.265
r_lrange_other	6.264
r_scangle_it	5.559
r_scangle_other	5.555
r_scbond_it	3.791
r_scbond_other	3.77
r_mcangle_other	3.754
r_mcangle_it	3.75
r_mcbond_it	2.651
r_mcbond_other	2.65
r_angle_refined_deg	1.729
r_angle_other_deg	0.587
r_symmetry_xyhbond_nbd_refined	0.286
r_nbd_refined	0.235
r_nbd_other	0.216
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.185
r_symmetry_nbd_refined	0.128
r_symmetry_nbtor_other	0.093
r_chiral_restr	0.081
r_xyhbond_nbd_other	0.074
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	974
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms

Software

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