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Crystal Structure of a fatty acid decarboxylase from Kocuria marina in complex with myristic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 10 % w/v PEG400, 4 M NaCl and 0.1 M Hepes (pH 7.5). The protein was concentrated to 60 mg/mL in 100 mM potassium phosphate, 5 % (w/v) glycerol, 150 mM NaCl, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.85 56.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.722 α = 90 b = 88.722 β = 90 c = 117.975 γ = 120
Symmetry Space Group P 31 2 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 2M 2023-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.97718 LNLS SIRIUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.05 46.79 100 0.098 0.1 1 18.07 20 34276 55.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.17 2.967 3.0460000000000003 0.455
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 46.79 1.35 34273 1714 99.97 0.2028 0.2016 0.2268 0.2086 60.26
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 12.3911 f_angle_d 0.6273 f_chiral_restr 0.0404 f_plane_restr 0.0051 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3330 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing