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Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L co-crystallized with Silver Nitrate (1 molecule in assymetric unit)
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 8.5 294 2M Ammonium Sulfate and 100 mM Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.809 α = 90 b = 126.809 β = 90 c = 72.981 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 2023-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 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 2.1 109.82 100 0.18 0.187 0.052 0.997 11.3 12.5 39777
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 2.1 2.16 100 0.931 0.977 0.293 0.856 10.8
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 2.1 60.86 37612 2139 99.98 0.17882 0.17705 0.1857 0.21133 0.215 RANDOM 26.051
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] -0.98 -0.49 -0.98 3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.41 r_dihedral_angle_2_deg 9.728 r_dihedral_angle_1_deg 7.102 r_long_range_B_refined 4.4 r_long_range_B_other 4.341 r_scangle_other 3.27 r_mcangle_it 2.054 r_mcangle_other 2.054 r_scbond_it 2.026 r_scbond_other 2.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.41 r_dihedral_angle_2_deg 9.728 r_dihedral_angle_1_deg 7.102 r_long_range_B_refined 4.4 r_long_range_B_other 4.341 r_scangle_other 3.27 r_mcangle_it 2.054 r_mcangle_other 2.054 r_scbond_it 2.026 r_scbond_other 2.025 r_mcbond_it 1.346 r_mcbond_other 1.346 r_angle_refined_deg 1.233 r_angle_other_deg 0.432 r_chiral_restr 0.061 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 3997 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction