8OIB

Trichomonas vaginalis riboside hydrolase in complex with glycerol

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	4.85	291.15	200 mM ammonium citrate dibasic pH 4.85, 15% w/v PEG 5000 monomethyl ether, 17.5% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.034	α = 90
b = 156.998	β = 90.562
c = 88.729	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 S 9M		2021-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9762	ESRF	ID30B

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	2.44	88.73	98	0.086	0.058	0.993	6.1	3		50817

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	2.44	2.48	99.2		0.473	0.317	0.848	2.1	3.1

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	2.44	88.725	50806	2482	98.011	0.19	0.1885	0.2255	55.063

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]
3.118		-0.311	-0.622		-2.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.75
r_dihedral_angle_6_deg	14.573
r_lrange_it	9.102
r_lrange_other	9.098
r_scangle_it	6.971
r_scangle_other	6.97
r_dihedral_angle_1_deg	6.896
r_mcangle_it	5.763
r_mcangle_other	5.763
r_dihedral_angle_2_deg	5.573
r_scbond_it	4.454
r_scbond_other	4.454
r_mcbond_it	3.754
r_mcbond_other	3.751
r_angle_refined_deg	1.179
r_angle_other_deg	0.4
r_symmetry_nbd_refined	0.3
r_nbd_other	0.213
r_nbd_refined	0.209
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.174
r_ncsr_local_group_2	0.081
r_ncsr_local_group_4	0.08
r_ncsr_local_group_6	0.079
r_symmetry_nbtor_other	0.077
r_ncsr_local_group_5	0.076
r_ncsr_local_group_3	0.073
r_ncsr_local_group_1	0.068
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_symmetry_xyhbond_nbd_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10610
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	28

Software

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