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Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 co-crystallized with Silver Nitrate
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 5.6 294 25% PEG 4000, 100 mM Sodium Citrate pH 5.6 and 0.2 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.06 40.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.122 α = 90 b = 121.122 β = 90 c = 174.556 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 2023-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 2.7 174.56 99.9 0.177 0.187 0.059 0.998 15.9 18.5 41277
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 2.7 2.81 99.1 1.137 1.243 0.493 0.717 2.4 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.7 104.89 39227 2004 99.86 0.20381 0.20152 0.2076 0.24933 0.2526 RANDOM 56.365
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] -0.36 -0.18 -0.36 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.975 r_long_range_B_refined 7.644 r_long_range_B_other 7.644 r_dihedral_angle_1_deg 7.4 r_scangle_other 5.73 r_dihedral_angle_2_deg 5.646 r_mcangle_it 4.782 r_mcangle_other 4.782 r_scbond_it 3.622 r_scbond_other 3.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.975 r_long_range_B_refined 7.644 r_long_range_B_other 7.644 r_dihedral_angle_1_deg 7.4 r_scangle_other 5.73 r_dihedral_angle_2_deg 5.646 r_mcangle_it 4.782 r_mcangle_other 4.782 r_scbond_it 3.622 r_scbond_other 3.608 r_mcbond_it 3.163 r_mcbond_other 3.156 r_angle_refined_deg 1.225 r_angle_other_deg 0.445 r_chiral_restr 0.057 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 7303 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing