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Psychrophilic laccase (multicopper oxidase) from Oenococcus oeni 229 without Histag
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 18% PEG 10000, 20% glycerol, 100 mM Tris-HCl pH 8.5 and 100 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.2289659 44.84415
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.672 α = 90 b = 97.865 β = 91.65 c = 96.098 γ = 90
Symmetry Space Group P 1 21 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 2023-03-29 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 3 68.65 97.8 0.299 0.336 0.15 0.912 4.4 4.7 19139
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 3.18 97.8 0.788 0.889 0.401 0.66 4.7
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 68.65 18254 847 97.25 0.22139 0.21929 0.2214 0.26629 0.2617 RANDOM 20.207
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] -2.56 -0.21 -3.46 6.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.457 r_dihedral_angle_1_deg 6.458 r_dihedral_angle_2_deg 5.276 r_long_range_B_refined 3.936 r_long_range_B_other 3.935 r_scangle_other 1.553 r_mcangle_it 1.266 r_mcangle_other 1.266 r_angle_refined_deg 1.132 r_scbond_it 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.457 r_dihedral_angle_1_deg 6.458 r_dihedral_angle_2_deg 5.276 r_long_range_B_refined 3.936 r_long_range_B_other 3.935 r_scangle_other 1.553 r_mcangle_it 1.266 r_mcangle_other 1.266 r_angle_refined_deg 1.132 r_scbond_it 0.925 r_scbond_other 0.925 r_mcbond_it 0.727 r_mcbond_other 0.727 r_angle_other_deg 0.468 r_chiral_restr 0.048 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 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 7405 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing