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2,3-Dihydroxybenzoate Decarboxylase of Aspergillus oryzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.1 M magnesium chloride 0.1 M Na HEPES 7.5 10 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.96 37.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.794 α = 90 b = 99.794 β = 90 c = 129.177 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 6M 2017-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.21 47.64 83.12 0.1235 0.986 6.99 4.2 165014 11.53
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 1.21 1.254 0.764 1.07
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DVT 1.21 47.64 1.34 163884 8097 83.12 0.1426 0.1411 0.1407 0.1713 0.1703 15.11
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 19.1397 f_angle_d 0.9937 f_chiral_restr 0.076 f_plane_restr 0.0076 f_bond_d 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5510 Nucleic Acid Atoms Solvent Atoms 1187 Heterogen Atoms 3
Software Software Software Name Purpose DIALS data reduction PHENIX refinement Coot model building