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Crystal Structure of FMN-dependent Cysteine Decarboxylases TvaF from Thioviridamide Biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Two micro liters of protein solution containing 7 mg/ml Tvaf in 20 mM Tris, pH 8.0, 50 mM NaCl, was mixed with 2 micro liters of well solution containing 0.1 M Sodium chloride, 0.1M Bicine pH 9.0, and 30% PEG 500 MME (vol/vol). The crystallization drop was incubated against 100 micro liters of well solution.
Crystal Properties Matthews coefficient Solvent content 5.23 76.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.915 α = 90 b = 216.915 β = 90 c = 216.915 γ = 90
Symmetry Space Group F 41 3 2
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 S 6M 2018-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9793 SSRF BL18U1
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 2.24 76.691 100 0.999 11.5 29.8 21611
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 2.24 2.31 0.395
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 THROUGHOUT 1G63 2.24 76.691 1.39 21582 1124 99.94 0.2166 0.2158 0.2183 0.2315 0.2357
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 13.521 f_angle_d 0.89 f_chiral_restr 0.056 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1190 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing