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Crystal structure of a laccase-like multicopper oxidase McoG from Aspergillus niger bound to zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 296 20% PEG3000, 0.2 M zinc acetate, 0.1 M imidazole pH=8.0
Crystal Properties Matthews coefficient Solvent content 3.08 60.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.446 α = 90 b = 128.158 β = 90 c = 134.676 γ = 90
Symmetry Space Group I 2 2 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 CCD OXFORD ONYX CCD 2011-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.505
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.65 29.398 99.6 0.128 10.79 3.6 42878 -3 24.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.81 98.5 0.452 2.92
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 1GW0 2.65 20 21395 1154 99.5 0.189 0.185 0.1887 0.267 0.2579 RANDOM 41.8
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] -0.54 0.81 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.784 r_dihedral_angle_4_deg 20.537 r_dihedral_angle_3_deg 16.68 r_dihedral_angle_1_deg 9.179 r_mcangle_it 4.445 r_scbond_it 3.403 r_mcbond_it 2.923 r_angle_refined_deg 1.888 r_chiral_restr 0.116 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.784 r_dihedral_angle_4_deg 20.537 r_dihedral_angle_3_deg 16.68 r_dihedral_angle_1_deg 9.179 r_mcangle_it 4.445 r_scbond_it 3.403 r_mcbond_it 2.923 r_angle_refined_deg 1.888 r_chiral_restr 0.116 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4354 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction