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Structural Studies Reveals the Inactivation of E. coli L-aspartate aminotransferase (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) via two mechanisms at pH 6.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AMQ PDB ENTRY 1AMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6 298 25 mM potassium phosphate, 43% saturated ammonium sulfate, 20 mM SADTA, pH 6.0, EVAPORATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.623 α = 90 b = 85.135 β = 90 c = 78.849 γ = 90
Symmetry Space Group C 2 2 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 2005-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.4 77 97 0.062 17.4 5.7 93239
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 1.4 1.45 99.8 0.571 2.7 5.4 10020
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AMQ 1.4 76.92 2 93239 4903 96.42 0.15556 0.15386 0.152 0.18836 0.1866 RANDOM 23.351
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] -1.03 0.32 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.75 r_dihedral_angle_4_deg 18.82 r_dihedral_angle_3_deg 13.056 r_scangle_it 5.887 r_dihedral_angle_1_deg 5.86 r_scbond_it 4.361 r_mcangle_it 2.847 r_mcbond_it 1.995 r_angle_refined_deg 1.923 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.75 r_dihedral_angle_4_deg 18.82 r_dihedral_angle_3_deg 13.056 r_scangle_it 5.887 r_dihedral_angle_1_deg 5.86 r_scbond_it 4.361 r_mcangle_it 2.847 r_mcbond_it 1.995 r_angle_refined_deg 1.923 r_nbtor_refined 0.319 r_nbd_refined 0.256 r_symmetry_hbond_refined 0.252 r_symmetry_vdw_refined 0.234 r_xyhbond_nbd_refined 0.218 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2947 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing