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Crystal structure of ACAT2 in complex with ZH-2-077
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 10% v/v 2-Propanol, 0.1 M BICINE pH 8.5, 30% w/v Polyethylene glycol 1,500
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.306 α = 90 b = 128.337 β = 90 c = 128.526 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER2 X 1M 2025-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 0.97 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.5 30 100 0.162 0.109 0.177 0.069 11.57 6.3 32826
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 2.5 2.54 99.8 0.76 0.82 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1WL4 2.5 28.59 27207 1498 87.29 0.19343 0.19104 0.1968 0.23721 0.241 RANDOM 40.707
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] -0.27 1.26 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.291 r_dihedral_angle_2_deg 7.034 r_dihedral_angle_1_deg 6.842 r_long_range_B_refined 5.806 r_long_range_B_other 5.806 r_scangle_other 3.898 r_mcangle_it 3.282 r_mcangle_other 3.282 r_scbond_it 2.321 r_scbond_other 2.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.291 r_dihedral_angle_2_deg 7.034 r_dihedral_angle_1_deg 6.842 r_long_range_B_refined 5.806 r_long_range_B_other 5.806 r_scangle_other 3.898 r_mcangle_it 3.282 r_mcangle_other 3.282 r_scbond_it 2.321 r_scbond_other 2.321 r_mcbond_it 1.995 r_mcbond_other 1.994 r_angle_refined_deg 1.276 r_angle_other_deg 0.451 r_chiral_restr 0.057 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 5742 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement SCALA data scaling HKL-2000 data reduction PDB_EXTRACT data extraction MOLREP phasing