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Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L 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 294 1.6M Ammonium Sulphate
1M Lithium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.86 57.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.524 α = 90 b = 126.524 β = 90 c = 74.027 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 2019-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97917 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 48.14 100 0.166 0.173 0.05 0.996 9.2 11.7 46387
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 2.05 100 1.138 1.188 0.34 0.74 12
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 48.14 44003 2321 99.9 0.2107 0.20926 0.23774 0.2518 RANDOM 31.953
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] -1.18 -0.59 -1.18 3.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.141 r_dihedral_angle_2_deg 8.96 r_dihedral_angle_1_deg 7.026 r_long_range_B_refined 5.3 r_long_range_B_other 5.295 r_scangle_other 3.867 r_mcangle_it 2.79 r_mcangle_other 2.79 r_scbond_it 2.288 r_scbond_other 2.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.141 r_dihedral_angle_2_deg 8.96 r_dihedral_angle_1_deg 7.026 r_long_range_B_refined 5.3 r_long_range_B_other 5.295 r_scangle_other 3.867 r_mcangle_it 2.79 r_mcangle_other 2.79 r_scbond_it 2.288 r_scbond_other 2.288 r_mcbond_it 1.777 r_mcbond_other 1.776 r_angle_refined_deg 1.243 r_angle_other_deg 0.445 r_chiral_restr 0.061 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 4014 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction