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Torpedo californica acetylcholinesterase in complex with a non-chiral donepezil-like inhibitor 17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 MES 100 mM, pH 6.2
PEG 200 30%
Crystal Properties Matthews coefficient Solvent content 4.01 69.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.53 α = 90 b = 111.53 β = 90 c = 136.88 γ = 120
Symmetry Space Group P 31 2 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 DECTRIS PILATUS 2M 2016-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 2.17 78.92 100 0.119 9.2 5.9 52442
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 2.17 2.29 100 0.526 3.1 5.8
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 5E4T 2.17 55.9 49664 2705 99.9 0.172 0.17 0.1775 0.21 0.2124 RANDOM 30.66
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] 0.85 0.85 0.85 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.003 r_dihedral_angle_4_deg 16.832 r_dihedral_angle_3_deg 14.57 r_long_range_B_refined 7.239 r_long_range_B_other 7.175 r_dihedral_angle_1_deg 6.762 r_scangle_other 6.187 r_scbond_it 4.24 r_scbond_other 4.239 r_mcangle_other 3.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.003 r_dihedral_angle_4_deg 16.832 r_dihedral_angle_3_deg 14.57 r_long_range_B_refined 7.239 r_long_range_B_other 7.175 r_dihedral_angle_1_deg 6.762 r_scangle_other 6.187 r_scbond_it 4.24 r_scbond_other 4.239 r_mcangle_other 3.625 r_mcangle_it 3.621 r_mcbond_it 2.626 r_mcbond_other 2.616 r_angle_refined_deg 2.037 r_angle_other_deg 0.995 r_chiral_restr 0.127 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 4206 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing