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Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit, with inhibitor tropolone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y9W PDB ENTRY 2Y9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 10% PEG 4000, 100 MM NA ACETATE PH 4.6, 5 MM HOLMIUM CHLORIDE.
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.84 α = 90 b = 104.82 β = 110.45 c = 119.36 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 100 CCD MARMOSAIC 225 mm CCD 2008-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.78 58 89.6 0.24 3.5 2.7 54004
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 2.78 2.93 89.7 0.62 1.6 2.6
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 PDB ENTRY 2Y9W 2.78 58.03 51269 2715 89.1 0.238 0.235 0.2425 0.289 0.296 RANDOM 52.7
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] 0.13 -0.03 0.02 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_3_deg 15.646 r_dihedral_angle_4_deg 12.274 r_dihedral_angle_1_deg 4.979 r_angle_refined_deg 0.95 r_scangle_it 0.533 r_scbond_it 0.491 r_mcangle_it 0.266 r_mcbond_it 0.143 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_3_deg 15.646 r_dihedral_angle_4_deg 12.274 r_dihedral_angle_1_deg 4.979 r_angle_refined_deg 0.95 r_scangle_it 0.533 r_scbond_it 0.491 r_mcangle_it 0.266 r_mcbond_it 0.143 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_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 17052 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing