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Crystal Structure of human MAO B in complex with (Z)-N-benzyl-1-(8-hydroxyquinolin-2-yl)methanimine oxide (inhibitor 19)
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 6.5 277.15 12 % (w/v) PEG 4000, 100 mM ADA buffer pH 6.5, 70 mM Lithium Sulfate, 4.5 mM Zwittergent 3-12
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.644 α = 90 b = 222.399 β = 90 c = 86.221 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 PILATUS3 2M 2021-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
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 2 47.34 99.4 0.17 0.207 0.117 0.99 7.2 5.3 84901
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 2 2.04 99.8 0.856 0.99 0.628 0.617 1.7 4.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2V5Z 2 47.34 84872 2205 99.156 0.167 0.1661 0.1755 0.2042 0.2104 21.933
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] 1.635 -1.223 -0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.018 r_dihedral_angle_other_3_deg 21.092 r_dihedral_angle_4_deg 15.624 r_dihedral_angle_3_deg 13.969 r_dihedral_angle_1_deg 6.727 r_lrange_it 5.52 r_lrange_other 5.446 r_scangle_it 4.158 r_scangle_other 4.157 r_scbond_it 2.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.018 r_dihedral_angle_other_3_deg 21.092 r_dihedral_angle_4_deg 15.624 r_dihedral_angle_3_deg 13.969 r_dihedral_angle_1_deg 6.727 r_lrange_it 5.52 r_lrange_other 5.446 r_scangle_it 4.158 r_scangle_other 4.157 r_scbond_it 2.688 r_scbond_other 2.688 r_mcangle_other 2.319 r_mcangle_it 2.318 r_angle_other_deg 1.764 r_angle_refined_deg 1.618 r_mcbond_it 1.617 r_mcbond_other 1.613 r_symmetry_xyhbond_nbd_refined 0.628 r_symmetry_nbd_refined 0.373 r_nbd_other 0.278 r_nbd_refined 0.201 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_other 0.178 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.169 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 689 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing