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Trichomonas vaginalis riboside hydrolase in complex with glycerol
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.44 88.725 50806 2482 98.011 0.19 0.1885 0.1962 0.2255 0.2314 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
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