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Computationally redesigend variant of Pyrrolysyl-tRNA Synthetase (Y306A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 293 0.05M L-Arginine, 0.05M L-Glutamic acid monosodium salt hydrate, 28% v/v PEG Smear Broad, 5% v/v Glycerol, drop ratio 1:1
Crystal Properties Matthews coefficient Solvent content 3.58 65.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.306 α = 90 b = 104.306 β = 90 c = 70.807 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 2023-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.7 45.17 99.92 0.2166 0.2225 0.05042 0.998 12.17 19.3 12180 71.64
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 2.7 2.797 99.92 3.112 3.239 0.7564 0.514 0.97 18.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 45.17 1.36 12173 609 99.94 0.218 0.2166 0.2161 0.2438 0.2443 73.82
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.1762 f_angle_d 0.4024 f_chiral_restr 0.0388 f_plane_restr 0.0041 f_bond_d 0.0012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2042 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction XDS data scaling PHASER phasing