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X-ray structure of the tryptophan lyase NosL in complex with bound tryptamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 14-20% PEG 3350, 0.2 M KBr, 1 mM 5'- deoxyadenosine, 1 mM L-methionine, 15 mg/mL SaNosL (protein buffer: 50 mM Tris pH 8; 150 mM NaCl and 2 mM DTT), 10 mM tryptamine
Crystal Properties Matthews coefficient Solvent content 2.62 52.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.53 α = 90 b = 47.14 β = 108.9 c = 113.9 γ = 90
Symmetry Space Group P 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 PILATUS3 6M 2017-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.7 47.048 99.5 0.062 13.09 4.01 199118
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 0.761
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 4R34 1.7 47.048 0.97 199118 9730 97.26 0.1638 0.1624 0.1633 0.1887 0.1896
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 17.583 f_angle_d 1.468 f_chiral_restr 0.123 f_bond_d 0.019 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5925 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 142
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing