8OIA

Trichomonas vaginalis riboside hydrolase in complex with D-ribose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.85291.15200 mM ammonium citrate dibasic pH 4.85, 15% PEG 3300
Crystal Properties
Matthews coefficientSolvent content
2.346.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.995α = 90
b = 135.622β = 104.691
c = 94.075γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2021-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.243.98199.90.3050.1360.9815.25.971792
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)
12.22.251001.6080.4250.4251.25.8

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 REPLACEMENTTHROUGHOUT2.343.98162854322299.870.2360.2340.269931.968
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]
-0.8970.411-1.0781.548
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.421
r_dihedral_angle_3_deg14.992
r_dihedral_angle_1_deg6.986
r_lrange_it5.875
r_lrange_other5.875
r_dihedral_angle_2_deg5.361
r_scangle_it3.931
r_scangle_other3.931
r_mcangle_it3.259
r_mcangle_other3.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.421
r_dihedral_angle_3_deg14.992
r_dihedral_angle_1_deg6.986
r_lrange_it5.875
r_lrange_other5.875
r_dihedral_angle_2_deg5.361
r_scangle_it3.931
r_scangle_other3.931
r_mcangle_it3.259
r_mcangle_other3.259
r_scbond_it2.541
r_scbond_other2.54
r_mcbond_it2.145
r_mcbond_other2.145
r_angle_refined_deg1.379
r_symmetry_xyhbond_nbd_refined0.465
r_angle_other_deg0.464
r_symmetry_nbd_refined0.256
r_nbd_other0.243
r_nbd_refined0.214
r_symmetry_nbd_other0.189
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.147
r_metal_ion_refined0.112
r_ncsr_local_group_20.087
r_ncsr_local_group_60.085
r_ncsr_local_group_10.083
r_ncsr_local_group_50.081
r_symmetry_nbtor_other0.076
r_chiral_restr0.068
r_ncsr_local_group_30.053
r_ncsr_local_group_40.049
r_chiral_restr_other0.039
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10753
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing