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Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant Y471L co-crystallized with Copper Chloride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XJ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294 0.5 M Ammonium Sulfate, 1 M Lithium Sulfate and 100 mM Sodium Citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.24 45.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.68 α = 90 b = 123.68 β = 90 c = 181.77 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 PIXEL DECTRIS EIGER X 16M 2024-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 2.6 107.11 100 0.116 0.123 0.039 0.998 13.8 10 50107
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 2.6 2.69 100 0.987 1.046 0.344 0.829 9.1
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 2.6 107.11 47589 2472 99.99 0.19128 0.18934 0.1947 0.22864 0.2313 RANDOM 55.565
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] 0.99 0.5 0.99 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.546 r_long_range_B_refined 7.704 r_long_range_B_other 7.703 r_dihedral_angle_1_deg 7.683 r_dihedral_angle_2_deg 7.198 r_scangle_other 5.638 r_mcangle_other 4.785 r_mcangle_it 4.784 r_scbond_it 3.628 r_scbond_other 3.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.546 r_long_range_B_refined 7.704 r_long_range_B_other 7.703 r_dihedral_angle_1_deg 7.683 r_dihedral_angle_2_deg 7.198 r_scangle_other 5.638 r_mcangle_other 4.785 r_mcangle_it 4.784 r_scbond_it 3.628 r_scbond_other 3.628 r_mcbond_it 3.2 r_mcbond_other 3.199 r_angle_refined_deg 1.29 r_angle_other_deg 0.48 r_chiral_restr 0.066 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 7363 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction