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Partially closed conformation of talaropentaene synthase cyclase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris-Cl pH 8.5, 0.1 M MgCl2, 30% PEG 4000, 0.2 M NDSB-211
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.809 α = 90 b = 61.942 β = 116.298 c = 81.297 γ = 90
Symmetry Space Group I 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 EIGER X 4M 2019-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 47.2 98.1 0.05 0.998 14.3 3.6 22448 22.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.232 0.927 4.2 3.7
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 7VTA 2 47.2 1.37 22445 1094 97.85 0.1827 0.1807 0.1813 0.224 0.2242 26.81
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 4.6176 f_angle_d 0.722 f_chiral_restr 0.0458 f_bond_d 0.007 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2246 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing