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Trichomonas vaginalis riboside hydrolase in complex with 5-methyluridine
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 291.15 90 mM PIPES pH 7.0, 90 mM MgCl2, 45 mM KCl, 1 mM NiSO4, 14% (w/v) PEG 5000 monomethyl ether
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.49 α = 90 b = 92.49 β = 90 c = 186.884 γ = 90
Symmetry Space Group P 43 2 2
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 PILATUS 6M Toroidal mirror 2021-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1
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 1.95 46.288 100 0.213 0.059 0.999 11.5 13.2 59963
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 1.95 2 3.966 1.112 0.537 1.3
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.95 46.288 59894 3026 99.985 0.175 0.1731 0.1837 0.2036 0.2098 46.226
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] -0.743 -0.743 1.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.451 r_dihedral_angle_3_deg 14.021 r_lrange_it 6.671 r_lrange_other 6.634 r_dihedral_angle_1_deg 6.305 r_scangle_other 4.833 r_scangle_it 4.832 r_dihedral_angle_2_deg 4.098 r_scbond_it 3.009 r_scbond_other 3.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.451 r_dihedral_angle_3_deg 14.021 r_lrange_it 6.671 r_lrange_other 6.634 r_dihedral_angle_1_deg 6.305 r_scangle_other 4.833 r_scangle_it 4.832 r_dihedral_angle_2_deg 4.098 r_scbond_it 3.009 r_scbond_other 3.008 r_mcangle_it 2.955 r_mcangle_other 2.955 r_mcbond_it 1.94 r_mcbond_other 1.937 r_dihedral_angle_other_3_deg 1.824 r_angle_refined_deg 1.029 r_angle_other_deg 0.359 r_nbd_refined 0.203 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.178 r_nbd_other 0.162 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.13 r_symmetry_nbd_refined 0.107 r_ncsr_local_group_1 0.08 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5425 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing