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Ancestral L-Lys oxidase (ligand free form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 12.5% (w/v) PEG3350, 0.1 M HEPES-NaOH (pH 7.5) and 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.441 α = 90 b = 80.462 β = 90 c = 173.8 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 PILATUS3 6M 2020-03-25 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) R Merge I (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 2.2 49.3 98.8 0.106 0.999 18.9 13.5 63996
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.31 0.846 0.868
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.2 49.3 63926 3243 98.607 0.216 0.2136 0.2186 0.2552 0.2609 38.326
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] 1.256 -1.054 -0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.213 r_dihedral_angle_4_deg 19.984 r_dihedral_angle_3_deg 16.039 r_dihedral_angle_1_deg 7.463 r_lrange_it 7.204 r_lrange_other 7.199 r_scangle_it 5.052 r_scangle_other 5.046 r_mcangle_it 4.651 r_mcangle_other 4.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.213 r_dihedral_angle_4_deg 19.984 r_dihedral_angle_3_deg 16.039 r_dihedral_angle_1_deg 7.463 r_lrange_it 7.204 r_lrange_other 7.199 r_scangle_it 5.052 r_scangle_other 5.046 r_mcangle_it 4.651 r_mcangle_other 4.651 r_scbond_it 3.219 r_scbond_other 3.215 r_mcbond_it 3.102 r_mcbond_other 3.101 r_angle_refined_deg 1.498 r_angle_other_deg 1.275 r_symmetry_nbd_refined 0.311 r_nbd_other 0.268 r_nbd_refined 0.198 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.155 r_chiral_restr 0.075 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.049 r_ncsr_local_group_1 0.036 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9529 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling AutoSol phasing