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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 LIQUID DIFFUSION 293 17% (w/v) PEG4000, 23% 2-propanole, 100 mM tri sodium citrate trihydrate pH5,5
Crystal Properties Matthews coefficient Solvent content 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.891 α = 90 b = 52.989 β = 91.665 c = 148.498 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 2021-08-06 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 20 90.6 0.076 11.2 3.2 77411
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 2.11 0.412
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 19.94 77410 3734 90.338 0.208 0.2063 0.2406 0.2375 25.179
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] -0.294 0.22 -0.609 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.191 r_dihedral_angle_4_deg 19.483 r_dihedral_angle_3_deg 15.948 r_dihedral_angle_1_deg 6.996 r_lrange_it 6.522 r_lrange_other 6.476 r_scangle_it 4.268 r_scangle_other 4.268 r_mcangle_it 3.296 r_mcangle_other 3.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.191 r_dihedral_angle_4_deg 19.483 r_dihedral_angle_3_deg 15.948 r_dihedral_angle_1_deg 6.996 r_lrange_it 6.522 r_lrange_other 6.476 r_scangle_it 4.268 r_scangle_other 4.268 r_mcangle_it 3.296 r_mcangle_other 3.295 r_scbond_it 2.7 r_scbond_other 2.699 r_mcbond_it 2.146 r_mcbond_other 2.146 r_angle_refined_deg 1.479 r_angle_other_deg 1.258 r_nbd_refined 0.193 r_nbd_other 0.193 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.159 r_nbtor_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.095 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_6 0.071 r_ncsr_local_group_3 0.066 r_chiral_restr 0.065 r_ncsr_local_group_1 0.064 r_ncsr_local_group_4 0.064 r_symmetry_xyhbond_nbd_other 0.037 r_ncsr_local_group_2 0.033 r_ncsr_local_group_5 0.031 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8688 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction SCALA data scaling MOLREP phasing