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Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant M455A-M456A soaked with Copper 2 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 4.6 294 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 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.115 α = 90 b = 123.115 β = 90 c = 179.736 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 1.37723 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 2.3 52.29 100 0.165 0.169 0.038 0.999 14.2 19.4 70560
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 2.3 2.35 100 2.162 2.218 0.492 0.829 19.9
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 2.3 52.29 67048 3443 99.96 0.18925 0.18788 0.1962 0.21705 0.2243 RANDOM 44.521
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] 0.83 0.42 0.83 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 7.299 r_long_range_B_refined 6.631 r_long_range_B_other 6.63 r_dihedral_angle_2_deg 5.921 r_scangle_other 4.755 r_mcangle_other 3.555 r_mcangle_it 3.554 r_scbond_it 2.934 r_scbond_other 2.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 7.299 r_long_range_B_refined 6.631 r_long_range_B_other 6.63 r_dihedral_angle_2_deg 5.921 r_scangle_other 4.755 r_mcangle_other 3.555 r_mcangle_it 3.554 r_scbond_it 2.934 r_scbond_other 2.934 r_mcbond_it 2.332 r_mcbond_other 2.33 r_angle_refined_deg 1.174 r_angle_other_deg 0.449 r_chiral_restr 0.062 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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 7322 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction