☰ Navigation Tabs
Thioesterase domain (GbnD6 TE domain) from the gladiolin PKS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22% PEG 8000 and 0.1 M CHES (pH 8.5).
Crystal Properties Matthews coefficient Solvent content 2.13 42.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.745 α = 90 b = 60.009 β = 95.794 c = 63.472 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER X 16M 2021-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 43.5 99.94 0.1551 0.995 9.87 8.7 19199
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 99.97 0.6518 0.847 2.38 8.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 43.5 19199 946 99.974 0.174 0.1719 0.1817 0.2221 0.2271 21.962
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] 0.054 0.011 0.008 -0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.496 r_dihedral_angle_3_deg 14.804 r_dihedral_angle_1_deg 6.785 r_dihedral_angle_2_deg 6.331 r_lrange_it 5.555 r_lrange_other 5.46 r_scangle_it 3.626 r_scangle_other 3.625 r_mcangle_other 3.121 r_mcangle_it 3.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.496 r_dihedral_angle_3_deg 14.804 r_dihedral_angle_1_deg 6.785 r_dihedral_angle_2_deg 6.331 r_lrange_it 5.555 r_lrange_other 5.46 r_scangle_it 3.626 r_scangle_other 3.625 r_mcangle_other 3.121 r_mcangle_it 3.117 r_scbond_it 2.334 r_scbond_other 2.333 r_mcbond_it 1.979 r_mcbond_other 1.962 r_angle_refined_deg 1.341 r_angle_other_deg 0.446 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_refined 0.195 r_nbd_other 0.192 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.063 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2275 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing