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Crystal structure of Thermoanaerobacterales bacterium monoamine oxidase in complex with benzylamine
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 2.1 41.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.473 α = 90 b = 100.242 β = 90 c = 120.901 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 2023-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
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 1.14 77.17 100 0.996 9.4 13 43665
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 2.2 2.257 0.813 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 2.2 77.17 41489 2051 99.84 0.18151 0.17871 0.1895 0.23956 0.248 RANDOM 38.629
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] -2.93 4.56 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.755 r_dihedral_angle_4_deg 16.838 r_dihedral_angle_3_deg 14.479 r_dihedral_angle_1_deg 6.728 r_long_range_B_other 6.673 r_long_range_B_refined 6.672 r_scangle_other 5.333 r_mcangle_it 4.153 r_mcangle_other 4.151 r_scbond_it 3.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.755 r_dihedral_angle_4_deg 16.838 r_dihedral_angle_3_deg 14.479 r_dihedral_angle_1_deg 6.728 r_long_range_B_other 6.673 r_long_range_B_refined 6.672 r_scangle_other 5.333 r_mcangle_it 4.153 r_mcangle_other 4.151 r_scbond_it 3.545 r_scbond_other 3.545 r_mcbond_it 2.952 r_mcbond_other 2.949 r_angle_other_deg 1.802 r_angle_refined_deg 1.637 r_chiral_restr 0.068 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 6700 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement