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Tetrapodal ancestor of L-amino acid oxidases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 in 50 mM HEPES (pH 7.4), 500 mM NaCl, and 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.83 67.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.515 α = 90 b = 94.515 β = 90 c = 190.062 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 2023-06-30 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 2.5 190.06 99.9 0.129 0.135 0.038 0.998 14.2 12.9 30578
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 2.5 2.6 99.4 2.009 2.089 0.567 0.636 13.5
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 2.5 84.63 28919 1582 99.9 0.20701 0.20491 0.2119 0.24578 0.2473 RANDOM 57.399
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] 0.77 0.77 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.427 r_dihedral_angle_2_deg 13.949 r_long_range_B_other 12.008 r_long_range_B_refined 12.005 r_scangle_other 9.489 r_dihedral_angle_1_deg 6.871 r_mcangle_it 6.554 r_mcangle_other 6.554 r_scbond_it 6.459 r_scbond_other 6.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.427 r_dihedral_angle_2_deg 13.949 r_long_range_B_other 12.008 r_long_range_B_refined 12.005 r_scangle_other 9.489 r_dihedral_angle_1_deg 6.871 r_mcangle_it 6.554 r_mcangle_other 6.554 r_scbond_it 6.459 r_scbond_other 6.439 r_mcbond_it 4.631 r_mcbond_other 4.631 r_angle_refined_deg 1.466 r_angle_other_deg 0.495 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 3878 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing