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Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 deletion 482-509 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 2M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.363 α = 90 b = 124.363 β = 90 c = 182.238 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 2021-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97895 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 3.2 107.7 100 0.299 0.316 0.102 0.988 8.9 9.5 27532
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 3.2 3.39 100 1.137 1.2 0.384 0.813 9.7
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 3.2 107.7 26136 1359 99.99 0.1619 0.15936 0.1679 0.20979 0.2129 RANDOM 56.676
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] 0.76 0.38 0.76 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.881 r_long_range_B_refined 8.306 r_long_range_B_other 8.306 r_dihedral_angle_1_deg 7.292 r_dihedral_angle_2_deg 6.254 r_scangle_other 5.677 r_mcangle_it 4.86 r_mcangle_other 4.86 r_scbond_it 3.431 r_scbond_other 3.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.881 r_long_range_B_refined 8.306 r_long_range_B_other 8.306 r_dihedral_angle_1_deg 7.292 r_dihedral_angle_2_deg 6.254 r_scangle_other 5.677 r_mcangle_it 4.86 r_mcangle_other 4.86 r_scbond_it 3.431 r_scbond_other 3.43 r_mcbond_it 2.994 r_mcbond_other 2.99 r_angle_refined_deg 1.214 r_angle_other_deg 0.434 r_chiral_restr 0.057 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 7288 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction