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Ancestral L-Lys oxidase (AncLLysO-2) L-Arg 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 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.258 α = 90 b = 77.214 β = 104.334 c = 93.258 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 1.6 45.2 98.1 1 26.6 6.6 140292
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 1.6 1.64 0.93
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 1.6 45.2 140292 7018 98.1 0.154 0.152 0.1646 0.186 0.1937 17.941
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 0.001 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.595 r_dihedral_angle_4_deg 18.733 r_dihedral_angle_3_deg 11.924 r_dihedral_angle_1_deg 6.78 r_lrange_it 5.289 r_lrange_other 4.978 r_scangle_it 3.594 r_scangle_other 3.59 r_mcangle_it 2.603 r_mcangle_other 2.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.595 r_dihedral_angle_4_deg 18.733 r_dihedral_angle_3_deg 11.924 r_dihedral_angle_1_deg 6.78 r_lrange_it 5.289 r_lrange_other 4.978 r_scangle_it 3.594 r_scangle_other 3.59 r_mcangle_it 2.603 r_mcangle_other 2.603 r_scbond_it 2.413 r_scbond_other 2.408 r_mcbond_it 1.789 r_mcbond_other 1.788 r_angle_refined_deg 1.739 r_angle_other_deg 1.574 r_nbd_refined 0.216 r_nbd_other 0.194 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.165 r_symmetry_nbd_refined 0.156 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.049 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 1530 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing