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100K 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 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.855 α = 90 b = 55.946 β = 110.882 c = 99.247 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 EIGER2 X 16M 2025-02-20 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 1.81 43.48 96.9 0.074 0.088 0.047 0.998 9.4 3.4 67064 26.81
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 1.81 1.86 98 1.671 1.983 1.054 0.301 1.2 3.4
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 FOURIER SYNTHESIS FREE R-VALUE 1.81 43.46 1.34 66958 3370 96.15 0.1816 0.1806 0.181 0.1993 0.1994 35.86
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 15.0591 f_angle_d 0.8159 f_chiral_restr 0.0498 f_plane_restr 0.0086 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4953 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement Aimless data scaling xia2 data reduction PDB_EXTRACT data extraction PHASER phasing