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Tetrapodal ancestor of L-amino acid oxidases co-crystallised with indole-3-pyruvate
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, SITTING DROP 293 50 mM HEPES (pH 7.4), 500 mM NaCl, and 10% (v/v) glycerol, 10 mM indole-3-pyruvate
Crystal Properties Matthews coefficient Solvent content 3.86 68.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.532 α = 90 b = 95.532 β = 90 c = 187.607 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 2023-11-02 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 2.98 47.81 100 0.2 0.227 0.063 0.996 10.7 12.8 18521
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 2.98 3.08 1.8 1.2 0.892 0.488 13.4
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 2.98 47.81 17510 948 99.95 0.22361 0.22017 0.2345 0.28909 0.2979 RANDOM
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] -0.42 -0.42 0.84
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.824 r_long_range_B_other 13.824 r_scangle_other 9.913 r_mcangle_it 7.697 r_mcangle_other 7.697 r_scbond_it 6.635 r_scbond_other 6.634 r_mcbond_it 5.099 r_mcbond_other 5.096 r_angle_refined_deg 1.432
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.824 r_long_range_B_other 13.824 r_scangle_other 9.913 r_mcangle_it 7.697 r_mcangle_other 7.697 r_scbond_it 6.635 r_scbond_other 6.634 r_mcbond_it 5.099 r_mcbond_other 5.096 r_angle_refined_deg 1.432 r_angle_other_deg 0.48 r_chiral_restr 0.063 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_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg 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 3878 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing