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Crystal structure of apo Klebsiella pneumoniae 3,4-dihydroxybenzoic acid decarboxylase (AroY)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 Morpheus II (Molecular Dimensions) H3
40 mM Polyamines (Spermine tetrahydrochloride, Spermidine trihydrochloride, 1,4-Diaminobutane dihydrochloride, DL-Ornithine monohydrochloride)
0.1 M Buffer system 4 (MOPSO/Bis-Tris)
50% precipitant mix 7 (20% w/v PEG 8000, 40% w/v 1,5-Pentanediol)
Crystal Properties Matthews coefficient Solvent content 2.81 56.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.88 α = 90 b = 209.7 β = 107.63 c = 116.02 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 PIXEL DECTRIS PILATUS 6M-F 2016-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92 Diamond I04
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 2.23 38.08 99.8 0.1145 8.2 3.4 180400
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.27 99.91 0.8952 0.566 1.27 3.5 17981
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.23 38.08 1.34 180312 8846 99.82 0.1647 0.1625 0.1751 0.2086 0.2155
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 12.557 f_angle_d 0.836 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22261 Nucleic Acid Atoms Solvent Atoms 1246 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing