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Engineered tyrosine synthase (TmTyrS1) derived from T. maritima TrpB with Ser bound as the amino-acrylate intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DVZ 5DVZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 1.2 M sodium phosphate monobasic,
0.8 M potassium phosphate dibasic,
0.1 M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS),
0.2 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.566 α = 90 b = 164.566 β = 90 c = 84.254 γ = 90
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 2022-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 45.97 100 0.16 0.04 0.998 12 13.5 88525 32.13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 2.43 0.67 0.577
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5DVZ 1.9 40.13 1.33 88501 4531 99.93 0.1713 0.1702 0.1696 0.1919 0.1916 34.62
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 14.5247 f_angle_d 1.4673 f_chiral_restr 0.0988 f_bond_d 0.019 f_plane_restr 0.0147
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5880 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing