8OIA

Trichomonas vaginalis riboside hydrolase in complex with D-ribose

X-RAY DIFFRACTION

---

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, SITTING DROP	4.85	291.15	200 mM ammonium citrate dibasic pH 4.85, 15% PEG 3300

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.995	α = 90
b = 135.622	β = 104.691
c = 94.075	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 PILATUS3 2M		2021-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	2.2	43.981	99.9	0.305	0.136	0.981	5.2	5.9		71792

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	2.2	2.25	100		1.608	0.425	0.425	1.2	5.8

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	2.3	43.981	62854	3222	99.87	0.236	0.234	0.2699	31.968

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]
-0.897		0.411	-1.078		1.548

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.421
r_dihedral_angle_3_deg	14.992
r_dihedral_angle_1_deg	6.986
r_lrange_it	5.875
r_lrange_other	5.875
r_dihedral_angle_2_deg	5.361
r_scangle_it	3.931
r_scangle_other	3.931
r_mcangle_it	3.259
r_mcangle_other	3.259
r_scbond_it	2.541
r_scbond_other	2.54
r_mcbond_it	2.145
r_mcbond_other	2.145
r_angle_refined_deg	1.379
r_symmetry_xyhbond_nbd_refined	0.465
r_angle_other_deg	0.464
r_symmetry_nbd_refined	0.256
r_nbd_other	0.243
r_nbd_refined	0.214
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.147
r_metal_ion_refined	0.112
r_ncsr_local_group_2	0.087
r_ncsr_local_group_6	0.085
r_ncsr_local_group_1	0.083
r_ncsr_local_group_5	0.081
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.068
r_ncsr_local_group_3	0.053
r_ncsr_local_group_4	0.049
r_chiral_restr_other	0.039
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	10753
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	72

Software

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