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Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant M455A-M456A soaked with Copper 10 minutes
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 294 85% 1 M Ammonium Sulfate, 0.1 M Sodium Acetate pH 4.6 and 15% of another condition with 0.2 Sodium Chloride, 0.1 M Phosphate-citrate pH 4.2 and 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.59 α = 90 b = 123.59 β = 90 c = 179.931 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 2024-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.37786 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 2.2 58.51 100 0.111 0.114 0.026 0.999 18.7 19.5 81174
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 2.2 2.24 100 1.504 1.544 0.346 0.856 19.4
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 2.2 58.51 77050 4069 99.98 0.18613 0.18447 0.1935 0.21705 0.2259 RANDOM 44.176
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] 0.66 0.33 0.66 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.911 r_dihedral_angle_1_deg 7.327 r_dihedral_angle_2_deg 7.026 r_long_range_B_refined 6.949 r_long_range_B_other 6.948 r_scangle_other 5.404 r_mcangle_it 3.865 r_mcangle_other 3.865 r_scbond_it 3.421 r_scbond_other 3.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.911 r_dihedral_angle_1_deg 7.327 r_dihedral_angle_2_deg 7.026 r_long_range_B_refined 6.949 r_long_range_B_other 6.948 r_scangle_other 5.404 r_mcangle_it 3.865 r_mcangle_other 3.865 r_scbond_it 3.421 r_scbond_other 3.413 r_mcbond_it 2.682 r_mcbond_other 2.681 r_angle_refined_deg 1.274 r_angle_other_deg 0.47 r_chiral_restr 0.067 r_gen_planes_refined 0.005 r_bond_refined_d 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 7314 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction