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Crystal structure of a Ruthenium and Copper-substituted small laccase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CG8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 1.8 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, 2% v/v polyethylene glycol monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 7.6 83.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.441 α = 90 b = 177.441 β = 90 c = 177.441 γ = 90
Symmetry Space Group P 43 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2023-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9789 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 30.91 99.79 0.191 0.996 21 43.1 55922 38.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 30.91 0.191 0.996
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 (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 3CG8 2.1 30.91 53253 2825 99.8 0.16951 0.16856 0.173 0.18794 0.1909 RANDOM 37.44
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.33 r_dihedral_angle_2_deg 9.555 r_long_range_B_refined 8.713 r_long_range_B_other 8.587 r_scangle_other 7.366 r_dihedral_angle_1_deg 7.135 r_scbond_it 5.369 r_scbond_other 5.367 r_mcangle_other 5.161 r_mcangle_it 5.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.33 r_dihedral_angle_2_deg 9.555 r_long_range_B_refined 8.713 r_long_range_B_other 8.587 r_scangle_other 7.366 r_dihedral_angle_1_deg 7.135 r_scbond_it 5.369 r_scbond_other 5.367 r_mcangle_other 5.161 r_mcangle_it 5.139 r_mcbond_it 3.97 r_mcbond_other 3.938 r_angle_refined_deg 2.185 r_angle_other_deg 0.758 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 2154 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing REFMAC refinement