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Tetrapodal ancestor of L-amino acid oxidase:Q225A single mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QSO
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 3.88 68.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.801 α = 90 b = 94.801 β = 90 c = 189.165 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 2025-06-19 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 2.79 189.17 98.4 0.152 0.169 0.069 0.939 6.7 5.6 21753
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 2.79 2.94 99.2 1.239 1.365 0.552 0.461 5.7
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 2.79 84.75 20536 1089 97.49 0.22237 0.21908 0.229 0.28445 0.2884 RANDOM 64.844
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] 0.05 0.05 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.894 r_long_range_B_other 11.926 r_long_range_B_refined 11.913 r_scangle_other 9.445 r_mcangle_it 8.409 r_mcangle_other 8.408 r_dihedral_angle_2_deg 7.747 r_dihedral_angle_1_deg 7.49 r_scbond_it 6.309 r_scbond_other 6.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.894 r_long_range_B_other 11.926 r_long_range_B_refined 11.913 r_scangle_other 9.445 r_mcangle_it 8.409 r_mcangle_other 8.408 r_dihedral_angle_2_deg 7.747 r_dihedral_angle_1_deg 7.49 r_scbond_it 6.309 r_scbond_other 6.307 r_mcbond_it 5.636 r_mcbond_other 5.636 r_angle_refined_deg 1.76 r_angle_other_deg 0.604 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 3874 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction PHASER phasing