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Crystal structure of human monoamine oxidase B (MAO B) in complex with dimethylphenyl-chromone-carboxamide
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 277 12% PEG4000, 100 mM ADA buffer pH 6.5, 70 mM lithium sulphate
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.182 α = 90 b = 222.753 β = 90 c = 86.482 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 X 2M 2016-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.987 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 47 99.4 0.164 0.102 10.2 6.8 117061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83
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 2v5z 1.8 47 114120 2940 99.97 0.16895 0.16817 0.1786 0.1987 0.2071 RANDOM 17.89
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] 1.25 -1.16 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.37 r_dihedral_angle_4_deg 14.731 r_dihedral_angle_3_deg 13.262 r_dihedral_angle_1_deg 6.086 r_long_range_B_refined 4.084 r_long_range_B_other 3.917 r_scangle_other 2.608 r_mcangle_it 1.623 r_mcangle_other 1.623 r_scbond_it 1.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.37 r_dihedral_angle_4_deg 14.731 r_dihedral_angle_3_deg 13.262 r_dihedral_angle_1_deg 6.086 r_long_range_B_refined 4.084 r_long_range_B_other 3.917 r_scangle_other 2.608 r_mcangle_it 1.623 r_mcangle_other 1.623 r_scbond_it 1.611 r_scbond_other 1.61 r_angle_other_deg 1.522 r_angle_refined_deg 1.481 r_mcbond_it 1.006 r_mcbond_other 1.005 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 7926 Nucleic Acid Atoms Solvent Atoms 842 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing