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Crystal structure of Arabidopsis thaliana Fatty Acid Thioesterase A in an apo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure provided by Syngenta, private communications.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.85 293 0.1M MES pH 6.85, 1.6M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.34 47.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.818 α = 90 b = 98.815 β = 90 c = 128.771 γ = 90
Symmetry Space Group I 2 2 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 EIGER2 XE 9M 2023-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9212 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.64 78.4 99.5 0.119 0.124 0.033 0.999 10.3 13.6 76807
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.67 98.8 3.327 3.476 0.993 0.395 11.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.64 78.4 72781 4025 99.41 0.21628 0.21394 0.2247 0.26069 0.2705 RANDOM 36.747
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] -0.42 -0.64 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.17 r_long_range_B_other 8.44 r_long_range_B_refined 8.435 r_dihedral_angle_2_deg 7.826 r_scangle_other 6.898 r_dihedral_angle_1_deg 6.175 r_scbond_it 4.376 r_scbond_other 4.347 r_mcangle_it 4.018 r_mcangle_other 4.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.17 r_long_range_B_other 8.44 r_long_range_B_refined 8.435 r_dihedral_angle_2_deg 7.826 r_scangle_other 6.898 r_dihedral_angle_1_deg 6.175 r_scbond_it 4.376 r_scbond_other 4.347 r_mcangle_it 4.018 r_mcangle_other 4.017 r_mcbond_it 2.895 r_mcbond_other 2.894 r_angle_refined_deg 1.6 r_angle_other_deg 0.545 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4243 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DIALS data scaling xia2 data reduction PHASER phasing