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Crystal structure of Thermoanaerobacterales bacterium monoamine oxidase in complex with putrescine
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 2.08 40.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.816 α = 90 b = 100.338 β = 90 c = 120.845 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) R Merge I (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 1.14 60.4 98.6 0.19 0.994 10.6 12.1 37362
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 2.3 0.99 0.704 2.5
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 2.3 60.4 35546 1763 98.44 0.20591 0.20259 0.2083 0.27542 0.2757 RANDOM 29.759
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] 1.17 1.25 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.548 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_1_deg 7.404 r_long_range_B_refined 5.276 r_long_range_B_other 5.27 r_scangle_other 3.781 r_mcangle_other 3.511 r_mcangle_it 3.51 r_scbond_it 2.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.548 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_1_deg 7.404 r_long_range_B_refined 5.276 r_long_range_B_other 5.27 r_scangle_other 3.781 r_mcangle_other 3.511 r_mcangle_it 3.51 r_scbond_it 2.508 r_scbond_other 2.508 r_mcbond_it 2.438 r_mcbond_other 2.435 r_angle_other_deg 1.78 r_angle_refined_deg 1.679 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 6691 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement