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Crystal Structure of human monoamine oxidase B in complex with Diphenylene iodonium (DPI)
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 PEG4000, lithium sulphate, ADA buffer
Crystal Properties Matthews coefficient Solvent content 2.6 52.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.486 α = 90 b = 222.544 β = 90 c = 85.567 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 PILATUS 6M 2019-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.98 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 46.69 98.7 0.98 4.2 3.8 106149
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 0.55
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2v5z 1.8 46.69 106149 5495 98.41 0.1894 0.1877 0.2239 0.2566 RANDOM 16.603
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] 0.68 -0.66 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.034 r_dihedral_angle_3_deg 13.859 r_dihedral_angle_4_deg 13.53 r_dihedral_angle_1_deg 6.998 r_angle_refined_deg 1.72 r_angle_other_deg 1.44 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.034 r_dihedral_angle_3_deg 13.859 r_dihedral_angle_4_deg 13.53 r_dihedral_angle_1_deg 6.998 r_angle_refined_deg 1.72 r_angle_other_deg 1.44 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 637 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing