Experiment: 9MG9

Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (glycerol bound)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A2EU62-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	291	JCSG+ A5: 0.2 M magnesium formate, pH 5.9, 20% (w/v) PEG 3350. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. glycerol acquired from the cryo. plate 14430 well A5 drop 2, Puck: PSL1005, Cryo: 80% crystallant + 20% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.806	α = 90
b = 50.947	β = 95.62
c = 153.15	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 XE 9M		2024-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9786	NSLS-II	19-ID

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	1.64	152.41	93.6	0.084	0.092	0.036	0.999	13.3	6.5		181573

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	1.64	1.68		100	1.183	1.281	0.486	0.648		6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.64	44.54	1.34	181517	9076	93.55	0.1535	0.1522	0.1554	0.1786	0.1787

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.65
f_angle_d	1.005
f_chiral_restr	0.06
f_bond_d	0.009
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10788
Nucleic Acid Atoms
Solvent Atoms	1171
Heterogen Atoms	78

Software

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