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Crystal structure of Pseudoalteromonas luteoviolacea L-amino acid oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350, 0.1 M Tris pH 7-8
Crystal Properties Matthews coefficient Solvent content 2.63 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.045 α = 90 b = 134.159 β = 90 c = 251.92 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS 6M 2020-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96862 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 2.8 48.49 100 0.053 0.995 8.3 3.4 38863 55.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.92 0.387 0.824 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 7C4K 2.8 47.17 1.34 38770 1959 99.85 0.2059 0.2025 0.2006 0.2699 0.2638 63.79
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 16.0308 f_angle_d 1.0032 f_chiral_restr 0.0547 f_plane_restr 0.0087 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9872 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 138
Software Software Software Name Purpose PHENIX refinement PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction