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Structure of a Human S-Adenosylmethionine Decarboxylase Self-processing Ester Intermediate and Mechanism of Putrescine Stimulation of Processing as Revealed by the H243A Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JEN PDB ENTRY 1JEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG 8000, dithiothreitol, tris(hydroxymethyl)aminomethane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.76 α = 90 b = 55.99 β = 109.72 c = 90.21 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 CCD SBC-1 1999-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 1.5 99 98.8 0.069 17.9 3.96 111488 111488 17.6
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 1.5 1.55 99.5 0.275 4.6 3.92 11200
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JEN 1.5 19.91 105350 105350 10521 93.7 0.221 0.221 0.215 0.2325 0.237 0.2521 RANDOM 16.9
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] -0.62 0.57 0.1 0.52
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_mcangle_it 2.49 c_scangle_it 2.43 c_scbond_it 1.64 c_mcbond_it 1.55 c_angle_deg 1.3 c_improper_angle_d 1.26 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5021 Nucleic Acid Atoms Solvent Atoms 806 Heterogen Atoms 28
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing