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Acyl-ACP thioesterase from Lemna paucicostata in complex with a spirolactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 20% (w/v) PEG4000, 23% 2-Propanole, 100mM tri sodium citrate trihydrate pH5,9
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.667 α = 90 b = 147.84 β = 90.052 c = 81.243 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 100 PIXEL Bruker PHOTON III 2021-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS DIAMOND MICROFOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 19.979 99.5 0.105 8.8 3.3 54778
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 0.423
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 2.3 19.979 54750 2679 99.385 0.259 0.2579 0.2607 0.2851 0.2856 29.39
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] -0.816 -0.378 1.423 -0.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.252 r_dihedral_angle_4_deg 21.012 r_dihedral_angle_3_deg 17.708 r_lrange_it 8.79 r_lrange_other 8.789 r_dihedral_angle_1_deg 8.062 r_mcangle_it 4.053 r_mcangle_other 4.052 r_scangle_it 3.759 r_scangle_other 3.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.252 r_dihedral_angle_4_deg 21.012 r_dihedral_angle_3_deg 17.708 r_lrange_it 8.79 r_lrange_other 8.789 r_dihedral_angle_1_deg 8.062 r_mcangle_it 4.053 r_mcangle_other 4.052 r_scangle_it 3.759 r_scangle_other 3.759 r_mcbond_it 2.461 r_mcbond_other 2.461 r_scbond_it 2.279 r_scbond_other 2.279 r_angle_refined_deg 1.451 r_angle_other_deg 1.221 r_nbd_other 0.268 r_symmetry_xyhbond_nbd_refined 0.252 r_symmetry_nbd_other 0.206 r_nbd_refined 0.195 r_symmetry_nbd_refined 0.171 r_xyhbond_nbd_refined 0.159 r_nbtor_refined 0.156 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.062 r_ncsr_local_group_1 0.06 r_ncsr_local_group_5 0.058 r_ncsr_local_group_6 0.058 r_ncsr_local_group_2 0.056 r_ncsr_local_group_3 0.044 r_ncsr_local_group_4 0.044 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8736 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction SCALA data scaling MOLREP phasing