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Crystal structure of Thermoanaerobacterales bacterium monoamine oxidase in complex with spermidine and its oxidation products
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG4000, 100 mM TRIS/HCl buffer pH 8.5, 200 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.06 40.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.335 α = 90 b = 94.456 β = 90 c = 127.74 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER R 1M 2023-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
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 63.95 99.8 0.999 20.3 19.8 77126
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 1.847 0.839 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 63.95 73229 3823 99.72 0.15548 0.15378 0.18933 0.1802 RANDOM 22.157
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] 0.26 -0.11 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.8 r_dihedral_angle_4_deg 17.601 r_dihedral_angle_3_deg 12.371 r_dihedral_angle_1_deg 6.264 r_long_range_B_refined 5.2 r_long_range_B_other 5.147 r_scangle_other 4.495 r_scbond_it 2.985 r_scbond_other 2.985 r_mcangle_other 2.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.8 r_dihedral_angle_4_deg 17.601 r_dihedral_angle_3_deg 12.371 r_dihedral_angle_1_deg 6.264 r_long_range_B_refined 5.2 r_long_range_B_other 5.147 r_scangle_other 4.495 r_scbond_it 2.985 r_scbond_other 2.985 r_mcangle_other 2.361 r_mcangle_it 2.358 r_angle_other_deg 1.941 r_mcbond_it 1.79 r_mcbond_other 1.781 r_angle_refined_deg 1.708 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 6715 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement