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Structure of latent apple tyrosinase (MdPPO1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Homology model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 15 mg/ml latent enzyme, 100 mM TRIS-HCl pH 8.25, 13 % PEG8000
Crystal Properties Matthews coefficient Solvent content 2.08 40.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.7 α = 90 b = 80.15 β = 90 c = 115.96 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2016-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.346 46.454 99.51 0.12 0.034 11.72 11.6 104709
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.346 1.39 97.6 1.174 0.377 2 117878
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Homology model 1.346 46.454 1.36 104707 5236 99.51 0.1447 0.1429 0.1793 0.1924
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 f_dihedral_angle_d 15.726 f_angle_d 1.287 f_chiral_restr 0.105 f_bond_d 0.014 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3574 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing