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Crystal structure of human Spermine Oxidase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 29.9999 %v/v MPD, 0.05 M MES
Crystal Properties Matthews coefficient Solvent content 4.18 70.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.919 α = 90 b = 190.919 β = 90 c = 43.574 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 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000010 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 2.395 165.34 79.1 0.167 0.167 9 11.8 28433
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.395 2.436 16.4 0.018 1.4 10.6
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 2.4 165.34 27492 941 79.09 0.1864 0.1854 0.1883 0.2141 0.216 RANDOM
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] -0.75 -0.37 -0.75 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.073 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_3_deg 13.853 r_dihedral_angle_1_deg 6.179 r_angle_refined_deg 1.358 r_angle_other_deg 1.107 r_chiral_restr 0.051 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.073 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_3_deg 13.853 r_dihedral_angle_1_deg 6.179 r_angle_refined_deg 1.358 r_angle_other_deg 1.107 r_chiral_restr 0.051 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3469 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 69
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing