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Crystal structure of queuine salvage enzyme DUF2419, apo form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.1 M Sodium malonate, 0.1 M HEPES, 0.5% (v/v) Jaffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 3.09 60.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.752 α = 90 b = 105.752 β = 90 c = 159.181 γ = 90
Symmetry Space Group P 41 21 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 2020-10-02 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2021-02-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97950 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97923, 0.95369, 0.97965 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 40 99.7 0.453 0.455 0.042 2.3 115.7 52930
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.8 6.216 6.261 0.736 0.637 70.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.1 37.48 48749 2521 96.22 0.1359 0.1343 0.1488 0.1659 0.1758 RANDOM 35.095
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] -0.66 -0.66 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.844 r_dihedral_angle_4_deg 18.245 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_1_deg 5.33 r_rigid_bond_restr 1.948 r_angle_refined_deg 1.303 r_angle_other_deg 1.298 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.844 r_dihedral_angle_4_deg 18.245 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_1_deg 5.33 r_rigid_bond_restr 1.948 r_angle_refined_deg 1.303 r_angle_other_deg 1.298 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5098 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing