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Crystal structure of laccase-like multicopper oxidase (LMCO) from Thermothelomyces thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold 2.0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M NH4Cl
18% w/v PEG 6000
0.1 M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.855 α = 90 b = 74.855 β = 90 c = 118.948 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER R 4M 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.9 118.95 100 0.105 0.114 0.043 0.999 14.8 12.9 51534
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 1.9 1.94 1.028 1.126 0.456 0.886 11.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Alphafold 2.0 1.9 74.967 51486 2567 99.996 0.153 0.1516 0.152 0.1847 0.1857 35.061
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] -1.867 -1.867 3.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.459 r_dihedral_angle_4_deg 22.054 r_dihedral_angle_3_deg 13.715 r_dihedral_angle_1_deg 8.025 r_lrange_it 5.532 r_lrange_other 5.481 r_scangle_it 2.98 r_scangle_other 2.98 r_mcangle_it 2.282 r_mcangle_other 2.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.459 r_dihedral_angle_4_deg 22.054 r_dihedral_angle_3_deg 13.715 r_dihedral_angle_1_deg 8.025 r_lrange_it 5.532 r_lrange_other 5.481 r_scangle_it 2.98 r_scangle_other 2.98 r_mcangle_it 2.282 r_mcangle_other 2.282 r_scbond_it 1.89 r_scbond_other 1.89 r_angle_refined_deg 1.7 r_mcbond_it 1.437 r_mcbond_other 1.437 r_angle_other_deg 1.358 r_nbd_refined 0.198 r_nbd_other 0.194 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.109 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.076 r_metal_ion_refined 0.038 r_symmetry_xyhbond_nbd_other 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4523 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction PHASER phasing