22FH | pdb_000022fh

Crystal structure of the reduced 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	5mM DTT, 0.2 M lithium sulfate monohydrate, 0.1 M HEPES (pH 5.5), and 25% polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.435	α = 90
b = 38.616	β = 90.044
c = 56.153	γ = 90

Symmetry
Space Group	P 1 2 1

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	1.77	38.724	98.3	0.995	7.9	6.2		22103

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	1.77	1.82			0.482

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	1.771	38.724	22102	1081	97.736	0.215	0.2116	0.217	0.2763	0.2727	35.604

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]
1.952		-0.109	-2.424		0.472

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.862
r_dihedral_angle_6_deg	13.017
r_lrange_other	7.786
r_lrange_it	7.784
r_dihedral_angle_1_deg	6.339
r_scangle_it	6.321
r_scangle_other	6.319
r_dihedral_angle_2_deg	4.879
r_mcangle_other	4.217
r_mcangle_it	4.203
r_scbond_it	4.089
r_scbond_other	4.082
r_mcbond_it	2.903
r_mcbond_other	2.891
r_angle_refined_deg	1.616
r_angle_other_deg	0.546
r_nbd_refined	0.219
r_nbd_other	0.195
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.166
r_symmetry_nbd_refined	0.087
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_refined	0.055
r_ncsr_local_group_1	0.037
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	1938
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms

Software

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