8QK1

Crystal structure of Trichuris suis beta-N-acetyl-D-hexosaminidase - HEX-2 in apo form

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	7.5	292	20% PEG 1500 0.15M potasium thiocynate 0.1M Tris pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.118	α = 90
b = 59.044	β = 114.486
c = 105.977	γ = 90

Symmetry
Space Group	C 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 EIGER X 16M		2022-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.55	43.74	99.9	0.067	0.08	0.043	0.999	14.1	6.5		17835			59.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.66	99.9		0.782	0.931	0.5	0.843	2.1	6.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.55	43.74	17268	836	96.734	0.193	0.1894	0.2594	42.658

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]
0.64		-0.307	0.12		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.451
r_dihedral_angle_6_deg	16.771
r_lrange_other	11.454
r_lrange_it	11.452
r_scangle_it	9.331
r_scangle_other	9.329
r_mcangle_it	8.122
r_mcangle_other	8.12
r_dihedral_angle_2_deg	7.398
r_dihedral_angle_1_deg	7.15
r_scbond_it	6.664
r_scbond_other	6.663
r_mcbond_it	5.855
r_mcbond_other	5.853
r_angle_refined_deg	1.996
r_angle_other_deg	0.64
r_symmetry_xyhbond_nbd_refined	0.322
r_nbd_refined	0.249
r_symmetry_nbd_other	0.238
r_nbtor_refined	0.205
r_nbd_other	0.187
r_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.126
r_xyhbond_nbd_other	0.093
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3688
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	1

Software

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