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Engineered holo tyrosine synthase (TmTyrS1) derived from T. maritima TrpB
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),
0.1 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.2 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.606 α = 90 b = 164.606 β = 90 c = 83.139 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 2022-01-21 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 2.05 39.15 100 0.07 0.02 1 21 13.6 69702 45.45
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 2.05 2.08 2.017 0.58 0.622
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 2.05 38.8 1.34 69678 3488 99.92 0.2171 0.2163 0.2163 0.2319 0.231 52.92
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 7.7125 f_angle_d 0.4698 f_chiral_restr 0.0415 f_plane_restr 0.0032 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5933 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing