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Crystal structure of Tyrosine decarboxylase in complex with the cofactor PLP and inhibitor carbidopa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Sodium malonate 0.8M
HEPES pH7.0 0.1M
TECP-HCl 0.005M
Glycerol 4%
Crystal Properties Matthews coefficient Solvent content 3.67 66.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.54 α = 90 b = 118.98 β = 90 c = 182.53 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2018-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.35 49.84 99.31 0.981 5.4 6.9 69325 57.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.35 3.47 0.8
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 3.35 49.84 1.37 69255 3464 99.36 0.216 0.2141 0.217 0.2514 0.2543 55.03
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 22.5931 f_angle_d 0.7212 f_chiral_restr 0.0469 f_bond_d 0.0051 f_plane_restr 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22785 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 186
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing