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Ancestral L-Lys oxidase (AncLLysO-2) L-Lys binding form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7X7I
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
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.408 α = 90 b = 77.4 β = 104.365 c = 93.414 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 2021-11-01 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 1.4 45.3 99.1 1 27.2 6.4 215621
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 1.4 1.47 0.939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 7X7I 1.4 45.3 215621 10663 99.1 0.159 0.158 0.1579 0.183 0.1827 15.786
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.208 r_dihedral_angle_4_deg 18.21 r_dihedral_angle_3_deg 12.227 r_dihedral_angle_1_deg 6.709 r_lrange_it 5.381 r_lrange_other 5.034 r_scangle_it 3.418 r_scangle_other 3.414 r_mcangle_it 2.539 r_mcangle_other 2.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.208 r_dihedral_angle_4_deg 18.21 r_dihedral_angle_3_deg 12.227 r_dihedral_angle_1_deg 6.709 r_lrange_it 5.381 r_lrange_other 5.034 r_scangle_it 3.418 r_scangle_other 3.414 r_mcangle_it 2.539 r_mcangle_other 2.539 r_scbond_it 2.301 r_scbond_other 2.297 r_angle_refined_deg 1.867 r_mcbond_it 1.675 r_mcbond_other 1.674 r_angle_other_deg 1.618 r_nbd_refined 0.222 r_symmetry_nbd_other 0.19 r_nbd_other 0.187 r_nbtor_refined 0.186 r_symmetry_nbd_refined 0.182 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_other 0.128 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.086 r_xyhbond_nbd_other 0.035 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 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 1621 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing