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Determination of the structure of active tyrosinase from bacterium Verrucomicrobium spinosum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z11 4Z11, 4Z12, 5CE9 experimental model PDB 4Z12 4Z11, 4Z12, 5CE9 experimental model PDB 5CE9 4Z11, 4Z12, 5CE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M ammonium sulfate, 0.1 M MES pH 6.5, 30% w/v PEG5000MME
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.298 α = 90 b = 63.443 β = 97.25 c = 117.311 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS EIGER2 X 16M 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.64 116.37 98.2 0.998 9.8 6.7 75699
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.67 0.362
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 4Z11, 4Z12, 5CE9 1.64 116.37 71195 3875 97.35 0.1922 0.1904 0.2017 0.2243 0.2352 RANDOM 25.752
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] 3.2 0.74 -1.32 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_4_deg 18.653 r_dihedral_angle_3_deg 12.649 r_dihedral_angle_1_deg 6.89 r_angle_refined_deg 1.586 r_angle_other_deg 1.406 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_4_deg 18.653 r_dihedral_angle_3_deg 12.649 r_dihedral_angle_1_deg 6.89 r_angle_refined_deg 1.586 r_angle_other_deg 1.406 r_chiral_restr 0.096 r_bond_refined_d 0.01 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 5179 Nucleic Acid Atoms Solvent Atoms 692 Heterogen Atoms 26
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing