8OIB

Trichomonas vaginalis riboside hydrolase in complex with glycerol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q8F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.85291.15200 mM ammonium citrate dibasic pH 4.85, 15% w/v PEG 5000 monomethyl ether, 17.5% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.2745.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.034α = 90
b = 156.998β = 90.562
c = 88.729γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2021-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9762ESRFID30B

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4488.73980.0860.0580.9936.1350817
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)RedundancyNumber Unique Reflections (All)
12.442.4899.20.4730.3170.8482.13.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.4488.72550806248298.0110.190.18850.225555.063
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
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.75
r_dihedral_angle_6_deg14.573
r_lrange_it9.102
r_lrange_other9.098
r_scangle_it6.971
r_scangle_other6.97
r_dihedral_angle_1_deg6.896
r_mcangle_it5.763
r_mcangle_other5.763
r_dihedral_angle_2_deg5.573
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.75
r_dihedral_angle_6_deg14.573
r_lrange_it9.102
r_lrange_other9.098
r_scangle_it6.971
r_scangle_other6.97
r_dihedral_angle_1_deg6.896
r_mcangle_it5.763
r_mcangle_other5.763
r_dihedral_angle_2_deg5.573
r_scbond_it4.454
r_scbond_other4.454
r_mcbond_it3.754
r_mcbond_other3.751
r_angle_refined_deg1.179
r_angle_other_deg0.4
r_symmetry_nbd_refined0.3
r_nbd_other0.213
r_nbd_refined0.209
r_symmetry_nbd_other0.185
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.174
r_ncsr_local_group_20.081
r_ncsr_local_group_40.08
r_ncsr_local_group_60.079
r_symmetry_nbtor_other0.077
r_ncsr_local_group_50.076
r_ncsr_local_group_30.073
r_ncsr_local_group_10.068
r_chiral_restr0.058
r_symmetry_xyhbond_nbd_other0.047
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_symmetry_xyhbond_nbd_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10610
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing