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Crystal structure of Peptidyl-tRNA Hydrolase 2 from Candidatus Lokiarchaeum sp. GC14_75
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB PDB_00001RLK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50 mM HEPES-NaOH pH 7.4, 19% (w/v) PEG3350, and 0.2 M Ammonium citrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.79 55.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.93 α = 90 b = 42.174 β = 90.12 c = 156.52 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M 2024-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.12 39.13 97.3 0.053 15 3.3 26728
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.25 0.169
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 MOLECULAR REPLACEMENT THROUGHOUT 2.12 39.13 25390 1337 97.31 0.20028 0.19924 0.2037 0.21992 0.228 RANDOM 46.319
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] 0.11 -0.25 0.63 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.99 r_dihedral_angle_2_deg 10.858 r_long_range_B_refined 9.336 r_long_range_B_other 9.293 r_scangle_other 7.835 r_dihedral_angle_1_deg 5.966 r_mcangle_it 5.557 r_mcangle_other 5.555 r_scbond_it 5.422 r_scbond_other 5.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.99 r_dihedral_angle_2_deg 10.858 r_long_range_B_refined 9.336 r_long_range_B_other 9.293 r_scangle_other 7.835 r_dihedral_angle_1_deg 5.966 r_mcangle_it 5.557 r_mcangle_other 5.555 r_scbond_it 5.422 r_scbond_other 5.421 r_mcbond_it 4.326 r_mcbond_other 4.324 r_angle_refined_deg 1.354 r_angle_other_deg 0.438 r_chiral_restr 0.06 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2793 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction BALBES phasing PDB_EXTRACT data extraction