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Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JS8 PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1 experimental model PDB 1LNL PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1 experimental model PDB 1WX2 PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1 experimental model PDB 1BT1 PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1
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 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.06 α = 90 b = 104.52 β = 90 c = 109.05 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r 2008-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.3 61.1 100 0.12 7.7 3.7 53813 32.6
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 2.3 2.42 100 0.55 2.3 3.5
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 PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1 2.3 47.13 50366 2699 100 0.184 0.181 0.1818 0.237 0.2368 RANDOM 33.27
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] -0.07 -0.01 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.451 r_dihedral_angle_3_deg 15.705 r_dihedral_angle_4_deg 13.663 r_dihedral_angle_1_deg 5.999 r_scangle_it 2.197 r_scbond_it 1.576 r_angle_refined_deg 1.164 r_mcangle_it 0.845 r_mcbond_it 0.437 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.451 r_dihedral_angle_3_deg 15.705 r_dihedral_angle_4_deg 13.663 r_dihedral_angle_1_deg 5.999 r_scangle_it 2.197 r_scbond_it 1.576 r_angle_refined_deg 1.164 r_mcangle_it 0.845 r_mcbond_it 0.437 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 8518 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing