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Crystal structure of the Saccharomyces cerevisiae URH1p riboside hydrolase
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, SITTING DROP 8.5 291.15 100 mM TrisHCl, 800 mM LiCl, 32% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.05 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.284 α = 90 b = 140.284 β = 90 c = 81.343 γ = 120
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 EIGER X 9M CRLs, multilayer mirrors 2022-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 121.49 94.1 0.167 0.981 5.9 12.9 13763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.89 81.8 0.988 0.57 1.8 11.2
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 2.74 121.49 13542 714 56.1 0.188 0.1859 0.1951 0.2245 0.2319 Random selection 39.22
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] 0.035 0.017 0.035 -0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.069 r_dihedral_angle_6_deg 13.936 r_dihedral_angle_1_deg 6.789 r_lrange_it 4.743 r_lrange_other 4.743 r_dihedral_angle_2_deg 4.505 r_scangle_it 2.456 r_scangle_other 2.456 r_mcangle_it 1.97 r_mcangle_other 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.069 r_dihedral_angle_6_deg 13.936 r_dihedral_angle_1_deg 6.789 r_lrange_it 4.743 r_lrange_other 4.743 r_dihedral_angle_2_deg 4.505 r_scangle_it 2.456 r_scangle_other 2.456 r_mcangle_it 1.97 r_mcangle_other 1.97 r_scbond_it 1.449 r_scbond_other 1.449 r_mcbond_it 1.151 r_mcbond_other 1.149 r_angle_refined_deg 0.908 r_angle_other_deg 0.295 r_nbd_refined 0.199 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.177 r_nbd_other 0.176 r_symmetry_xyhbond_nbd_other 0.175 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.14 r_symmetry_nbtor_other 0.076 r_ncsr_local_group_1 0.059 r_chiral_restr 0.041 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5220 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing