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L-amino acid oxidase 4 (HcLAAO4) from the fungus Hebeloma cylindrosporum in complex with L-glutamate
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: 2.05 M (NH4)2SO4, 0.1 M sodium citrate, pH 7.0; drop with 1000 nl protein + 500 nl reservoir
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.76 α = 90 b = 130.79 β = 95.655 c = 107.3 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 EIGER X 4M 2022-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 2.1 50 99.2 0.106 0.997 12.45 7.1 134327 39.62
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 2.1 2.15 99.9 1.901 0.5 1.27 7.36
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 2.1 40.62 1.35 134297 6714 99.16 0.1751 0.174 0.1739 0.195 0.1949 43.78
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 11.4203 f_angle_d 0.5204 f_chiral_restr 0.0404 f_plane_restr 0.0039 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16787 Nucleic Acid Atoms Solvent Atoms 951 Heterogen Atoms 637
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing