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Tetrapodal ancestor of L-amino acid oxidases: W377I double mutant with phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QS0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.2 M sodium nitrate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.87 68.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.234 α = 90 b = 94.234 β = 90 c = 191.73 γ = 90
Symmetry Space Group P 43 21 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 PILATUS3 6M 2025-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.3 46.12 99.5 0.116 0.125 0.044 0.998 14 7.5 38980
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.8 1.081 1.158 0.401 0.579 7.9
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 2.3 46.12 37028 1875 99.23 0.17882 0.17691 0.1849 0.21707 0.2212 RANDOM 40.845
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.069 r_dihedral_angle_2_deg 9.793 r_long_range_B_refined 8.785 r_long_range_B_other 8.785 r_scangle_other 7.493 r_dihedral_angle_1_deg 6.666 r_scbond_it 5.018 r_scbond_other 5.017 r_mcangle_it 4.849 r_mcangle_other 4.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.069 r_dihedral_angle_2_deg 9.793 r_long_range_B_refined 8.785 r_long_range_B_other 8.785 r_scangle_other 7.493 r_dihedral_angle_1_deg 6.666 r_scbond_it 5.018 r_scbond_other 5.017 r_mcangle_it 4.849 r_mcangle_other 4.848 r_mcbond_it 3.353 r_mcbond_other 3.352 r_angle_refined_deg 1.773 r_angle_other_deg 0.621 r_chiral_restr 0.09 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3885 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing