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Engineered pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina mazei (Mm) in complex with ATP and AzGVAisoK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7G Pyrrolysine tRNA Synthetase bound to a pyrrolysine analogue (cyc) and ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM MES, 30% PEG 300
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.09 α = 90 b = 43.93 β = 119.28 c = 72.75 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 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 1.25 30 97.7 0.079 2.1 3.5 76312
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 1.25 1.35 96.4 0.551 3.5
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 1.25 30 72492 3815 97.91 0.16102 0.15988 0.1747 0.18263 0.1952 RANDOM 21.588
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] -0.56 -0.3 -0.67 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.09 r_dihedral_angle_4_deg 12.323 r_dihedral_angle_3_deg 11.583 r_dihedral_angle_1_deg 6.912 r_long_range_B_refined 3.225 r_long_range_B_other 3.011 r_scangle_other 2.436 r_mcangle_it 2.015 r_mcangle_other 2.014 r_scbond_it 1.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.09 r_dihedral_angle_4_deg 12.323 r_dihedral_angle_3_deg 11.583 r_dihedral_angle_1_deg 6.912 r_long_range_B_refined 3.225 r_long_range_B_other 3.011 r_scangle_other 2.436 r_mcangle_it 2.015 r_mcangle_other 2.014 r_scbond_it 1.985 r_scbond_other 1.967 r_mcbond_it 1.555 r_mcbond_other 1.551 r_angle_refined_deg 1.428 r_angle_other_deg 1.388 r_rigid_bond_restr 1.383 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2124 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing