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Crystal structure of human MAO B in complex with (E)-3-(4-nitrophenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (chalcone inhibitor, 4a)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B0V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 12% PEG4000, ADA buffer pH 6.5, 70 mM lithium sulphate, 8.5 mM Zwittergent 3-12
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.342 α = 90 b = 223.925 β = 90 c = 86.853 γ = 90
Symmetry Space Group C 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 S 9M 2023-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87 ESRF ID23-2
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 1.8 47.68 100 0.162 0.174 0.062 0.998 14.1 15.5 119203
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 1.8 1.83 0.962 1.032 0.367 0.823 3.6
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 1.8 47.68 119199 3000 99.952 0.145 0.1442 0.158 0.1727 0.1847 18.854
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] 0.278 -0.175 -0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.916 r_dihedral_angle_other_3_deg 20.79 r_dihedral_angle_4_deg 14.702 r_dihedral_angle_3_deg 13.138 r_dihedral_angle_1_deg 6.491 r_lrange_it 6.209 r_lrange_other 6.098 r_scangle_it 4.971 r_scangle_other 4.971 r_scbond_it 3.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.916 r_dihedral_angle_other_3_deg 20.79 r_dihedral_angle_4_deg 14.702 r_dihedral_angle_3_deg 13.138 r_dihedral_angle_1_deg 6.491 r_lrange_it 6.209 r_lrange_other 6.098 r_scangle_it 4.971 r_scangle_other 4.971 r_scbond_it 3.267 r_scbond_other 3.267 r_mcangle_other 2.368 r_mcangle_it 2.365 r_angle_other_deg 1.827 r_angle_refined_deg 1.757 r_mcbond_it 1.685 r_mcbond_other 1.679 r_symmetry_nbd_refined 1.116 r_nbd_other 0.285 r_nbd_refined 0.205 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.163 r_symmetry_xyhbond_nbd_other 0.13 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7926 Nucleic Acid Atoms Solvent Atoms 853 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing