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Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.4 293 PEG 10000, 0.1M cacodylate buffer, 0.2M calcium acetate, pH 6.4, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.862 α = 90 b = 166.915 β = 90 c = 185.894 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 53.3 122905 19.7
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 1YNF 1.95 53.3 125357 121063 4850 96.6 0.23 0.219 0.219 0.2178 0.246 0.2446 RANDOM 25.93
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] -3.79 0.84 2.95
RMS Deviations Key Refinement Restraint Deviation x_torsion_deg 23.4 x_angle_deg 1.3 x_torsion_impr_deg 0.77 x_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13704 Nucleic Acid Atoms Solvent Atoms 982 Heterogen Atoms 68
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing