8OI7

Trichomonas vaginalis riboside hydrolase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q8F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291.15	90 mM PIPES pH 7.0, 90 mM MgCl2, 45 mM KCl, 1 mM NiSO4, 14% (w/v) PEG 5000 monomethyl ether

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.344	α = 90
b = 92.344	β = 90
c = 185.111	γ = 90

Symmetry
Space Group	P 43 2 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	Toroidal mirror	2020-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9724	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.85	46.321	98.8	0.149	0.027	0.999	15.1	21.5		68295

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89	89.1		1.478	0.519	0.625	1.2	8.2

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	THROUGHOUT	1.85	46.321	68100	3455	98.583	0.185	0.1837	0.2011	41.685

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]
-1.47			-1.47		2.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.026
r_dihedral_angle_3_deg	13.557
r_dihedral_angle_1_deg	6.46
r_lrange_it	6.224
r_lrange_other	6.173
r_dihedral_angle_2_deg	4.99
r_scangle_it	3.721
r_scangle_other	3.72
r_mcangle_other	2.556
r_mcangle_it	2.555
r_scbond_it	2.261
r_scbond_other	2.261
r_mcbond_it	1.736
r_mcbond_other	1.64
r_angle_refined_deg	1.038
r_angle_other_deg	0.358
r_nbd_refined	0.204
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.171
r_xyhbond_nbd_refined	0.154
r_nbd_other	0.145
r_symmetry_nbd_refined	0.133
r_ncsr_local_group_1	0.098
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.056
r_chiral_restr	0.054
r_bond_refined_d	0.004
r_dihedral_angle_other_3_deg	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5468
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	26

Software

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