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Structure of human Spermine Oxidase in complex with a highly selective allosteric inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.01 M Na Acet, 0.06 M NaF
Crystal Properties Matthews coefficient Solvent content 4.38 71.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.755 α = 90 b = 193.755 β = 90 c = 44.332 γ = 120
Symmetry Space Group P 3 2 1
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 EIGER X 16M 2020-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000040 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.09 167.8 48.2 0.068 0.068 18.9 13 27031
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.095 2.4 70 1.407 1.407 2 15.5
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 none 2.09 167.8 25687 1345 48.18 0.1968 0.1946 0.1999 0.2385 0.2375 RANDOM 68.76
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] -0.42 -0.21 -0.42 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.477 r_dihedral_angle_4_deg 14.721 r_dihedral_angle_3_deg 14.562 r_dihedral_angle_1_deg 6.401 r_angle_refined_deg 1.372 r_angle_other_deg 1.127 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.477 r_dihedral_angle_4_deg 14.721 r_dihedral_angle_3_deg 14.562 r_dihedral_angle_1_deg 6.401 r_angle_refined_deg 1.372 r_angle_other_deg 1.127 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3621 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 81
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing