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Ancestral L-Lys oxidase (AncLLysO-2) ligand free form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350, 0.1 M NDSB-256
Crystal Properties Matthews coefficient Solvent content 2.09 41.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.246 α = 90 b = 76.533 β = 104.389 c = 92.708 γ = 90
Symmetry Space Group P 1 21 1
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 2021-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.55 44.9 99.8 0.998 12.6 6.6 155511
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.63 0.952
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.55 44.9 155157 7653 99.1 0.164 0.163 0.191 0.1982 20.92
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] -0.001 -0.004 0.001 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.802 r_dihedral_angle_4_deg 15.976 r_dihedral_angle_3_deg 11.824 r_dihedral_angle_1_deg 6.834 r_lrange_it 5.386 r_lrange_other 5.085 r_scangle_it 3.519 r_scangle_other 3.519 r_mcangle_it 2.684 r_mcangle_other 2.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.802 r_dihedral_angle_4_deg 15.976 r_dihedral_angle_3_deg 11.824 r_dihedral_angle_1_deg 6.834 r_lrange_it 5.386 r_lrange_other 5.085 r_scangle_it 3.519 r_scangle_other 3.519 r_mcangle_it 2.684 r_mcangle_other 2.684 r_scbond_other 2.389 r_scbond_it 2.388 r_mcbond_it 1.856 r_mcbond_other 1.846 r_angle_refined_deg 1.775 r_angle_other_deg 1.561 r_nbd_other 0.256 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.22 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.033 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9024 Nucleic Acid Atoms Solvent Atoms 1365 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling AutoSol phasing