☰ Navigation Tabs
L-amino acid oxidase 4 (HcLAAO4) from the fungus Hebeloma cylindrosporum in complex with N-epsilon-acetyl-L-lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ENI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 protein: 10 mg/ml; reservoir solution: 2.15 M (NH4)2SO4, 0.1 M sodium citrate, pH 7.0; drop with 200 nl protein + 200 nl reservoir
Crystal Properties Matthews coefficient Solvent content 2.41 48.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.88 α = 90 b = 132.12 β = 95.928 c = 107.32 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2022-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 50 98.8 0.08 0.999 13.42 6.24 214609 31.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 88 1.844 0.32 0.96 4.03
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.8 47.38 1.34 214559 10728 98.79 0.1553 0.1541 0.1535 0.1769 0.1764 37.98
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.9139 f_angle_d 0.8579 f_chiral_restr 0.0496 f_plane_restr 0.0079 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16795 Nucleic Acid Atoms Solvent Atoms 1502 Heterogen Atoms 579
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing