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Crystal structure of human Monoamine Oxidase B (MAO B) in complex with 7-[(4-{[(3,4-dimethoxybenzyl(methyl)amino]methyl}benzyl)oxy]-4-(hydroxymethyl)-2H-chromen-2-one) (LP1488)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 12% PEG4000, 100 mM ADA buffer pH 6.5, 70 mM lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.599 α = 90 b = 222.27 β = 90 c = 85.955 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 EIGER X 4M 2025-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96546 ESRF ID30B
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 1.6 86.1 100 0.086 0.102 0.055 0.999 16.1 6.6 164045 12.158
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 1.6 1.63 1.048 1.243 0.661 0.605 2
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 (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 1.6 86.1 159877 4158 99.97 0.1533 0.15252 0.167 0.183 0.1923 RANDOM 17.845
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] 0.73 -0.66 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.004 r_dihedral_angle_4_deg 15.088 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 6.584 r_long_range_B_refined 5.331 r_long_range_B_other 5.19 r_scangle_other 4.393 r_scbond_it 2.919 r_scbond_other 2.919 r_mcangle_it 2.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.004 r_dihedral_angle_4_deg 15.088 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 6.584 r_long_range_B_refined 5.331 r_long_range_B_other 5.19 r_scangle_other 4.393 r_scbond_it 2.919 r_scbond_other 2.919 r_mcangle_it 2.072 r_mcangle_other 2.072 r_angle_other_deg 1.878 r_angle_refined_deg 1.767 r_mcbond_it 1.498 r_mcbond_other 1.496 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 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 7926 Nucleic Acid Atoms Solvent Atoms 830 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing