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Engineered pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina barkeri (Mb) in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 30XL Engineered pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina mazei
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 100 mM MES, 10% Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.53 51.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.67 α = 90 b = 63.22 β = 95.05 c = 81.64 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 EIGER X 16M 2025-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.55 30 95.3 0.054 11.6 3.5 85191
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 1.55 1.65 96.5 0.776 2 3.6
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 1.55 30 80923 4259 95.34 0.18532 0.18377 0.1847 0.21444 0.2161 RANDOM 31.497
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] -1.09 -0.38 0.69 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.82 r_dihedral_angle_4_deg 13.081 r_dihedral_angle_3_deg 11.57 r_dihedral_angle_1_deg 6.257 r_long_range_B_refined 4.385 r_mcangle_it 2.883 r_scbond_it 2.579 r_mcbond_it 2.202 r_rigid_bond_restr 1.313 r_angle_refined_deg 0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.82 r_dihedral_angle_4_deg 13.081 r_dihedral_angle_3_deg 11.57 r_dihedral_angle_1_deg 6.257 r_long_range_B_refined 4.385 r_mcangle_it 2.883 r_scbond_it 2.579 r_mcbond_it 2.202 r_rigid_bond_restr 1.313 r_angle_refined_deg 0.986 r_chiral_restr 0.08 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4155 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing