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293K human S-adenosylmethionine decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 4mg/mL enzyme in 200mM NaCl 50mM HEPES pH 7.5 1:1 to reservoir solution containing 4-8% PEG 8000 and 50mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.07 36.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.418 α = 90 b = 45.876 β = 104.971 c = 72.248 γ = 90
Symmetry Space Group C 1 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 293 PIXEL DECTRIS EIGER2 S 16M 2025-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.16 37.41 98.7 0.306 0.331 0.123 0.977 5.1 7.1 16461 16.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.2 85.4 0.932 1.2 0.676 0.285 1.5 2.8
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 2.17 37.41 1.34 16253 815 98.22 0.2088 0.208 0.2083 0.2228 0.2234 29.11
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 16.3168 f_angle_d 0.9337 f_chiral_restr 0.1022 f_plane_restr 0.0077 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2461 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement Aimless data scaling xia2 data reduction PDB_EXTRACT data extraction PHASER phasing