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Tetrapodal ancestor of L-amino acid oxidases: W377I mutant bound to phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 50 mM HEPES, 500 mM NaCl, and 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.531 α = 90 b = 211.752 β = 90 c = 62.537 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS4 X 4M 2025-06-23 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) 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 1.84 47.95 100 0.156 0.074 0.999 7.1 6.4 86833
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.9 99.9 1.128 0.561 0.549 1.3 6.1
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 1.84 47.95 82386 4293 99.86 0.21389 0.21182 0.2192 0.25397 0.258 RANDOM 26.292
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] -1.85 0.08 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.457 r_dihedral_angle_4_deg 23.235 r_dihedral_angle_3_deg 15.919 r_dihedral_angle_1_deg 6.856 r_long_range_B_other 6.065 r_long_range_B_refined 6.063 r_scangle_other 4.51 r_scbond_it 2.883 r_scbond_other 2.883 r_mcangle_it 2.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.457 r_dihedral_angle_4_deg 23.235 r_dihedral_angle_3_deg 15.919 r_dihedral_angle_1_deg 6.856 r_long_range_B_other 6.065 r_long_range_B_refined 6.063 r_scangle_other 4.51 r_scbond_it 2.883 r_scbond_other 2.883 r_mcangle_it 2.791 r_mcangle_other 2.79 r_mcbond_other 1.918 r_mcbond_it 1.917 r_angle_refined_deg 1.548 r_angle_other_deg 1.325 r_chiral_restr 0.077 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_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 7690 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing