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Trichomonas vaginalis riboside hydrolase (His-tagged)
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 8.5 291.15 0.1 M bicine pH 8.5, 20% (w/v) PEG 5000 monomethyl ether, 3% sucrose
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.055 α = 105.081 b = 94.665 β = 89.959 c = 120.589 γ = 93.826
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 X 16M 2020-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.578 116.42 98.5 0.147 0.089 0.993 6.3 3.7 96699
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 2.578 2.623 98.2 1.432 0.855 0.361 0.9 3.8
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 116.418 75517 3857 98.572 0.211 0.2093 0.2125 0.2508 0.2504 Random 64.186
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] -1.629 0.695 -0.286 4.401 1.406 -3.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.533 r_dihedral_angle_6_deg 14.982 r_lrange_other 10.395 r_lrange_it 10.394 r_dihedral_angle_1_deg 7.451 r_dihedral_angle_2_deg 6.625 r_scangle_it 6.582 r_scangle_other 6.581 r_mcangle_it 6.08 r_mcangle_other 6.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.533 r_dihedral_angle_6_deg 14.982 r_lrange_other 10.395 r_lrange_it 10.394 r_dihedral_angle_1_deg 7.451 r_dihedral_angle_2_deg 6.625 r_scangle_it 6.582 r_scangle_other 6.581 r_mcangle_it 6.08 r_mcangle_other 6.08 r_scbond_it 4.173 r_scbond_other 4.173 r_mcbond_it 3.926 r_mcbond_other 3.926 r_angle_refined_deg 1.205 r_angle_other_deg 0.4 r_symmetry_xyhbond_nbd_refined 0.331 r_symmetry_nbd_refined 0.296 r_nbd_other 0.259 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_other 0.156 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.057 r_ncsr_local_group_10 0.044 r_ncsr_local_group_19 0.043 r_ncsr_local_group_5 0.041 r_ncsr_local_group_14 0.041 r_ncsr_local_group_1 0.04 r_ncsr_local_group_9 0.04 r_ncsr_local_group_11 0.04 r_ncsr_local_group_15 0.04 r_ncsr_local_group_3 0.039 r_ncsr_local_group_20 0.039 r_ncsr_local_group_4 0.038 r_ncsr_local_group_8 0.038 r_ncsr_local_group_13 0.037 r_ncsr_local_group_16 0.037 r_ncsr_local_group_21 0.037 r_ncsr_local_group_22 0.037 r_ncsr_local_group_23 0.037 r_ncsr_local_group_24 0.036 r_ncsr_local_group_25 0.035 r_ncsr_local_group_7 0.034 r_ncsr_local_group_12 0.034 r_ncsr_local_group_27 0.034 r_ncsr_local_group_2 0.033 r_ncsr_local_group_26 0.033 r_ncsr_local_group_6 0.032 r_ncsr_local_group_18 0.032 r_ncsr_local_group_28 0.03 r_ncsr_local_group_17 0.026 r_metal_ion_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_chiral_restr_other 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 21277 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing