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Mechanism of inactivation of E. coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA) pH 7.5
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 VAPOR DIFFUSION 7.5 297 Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.135 α = 90 b = 85.532 β = 90 c = 79.033 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.97 APS 14-BM-C
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 1.7 77.2 97.7 67102
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1.7 77.15 2 67102 53395 2851 97.83 0.15012 0.14827 0.1473 0.18519 0.1825 RANDOM 23.043
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] -0.59 0.55 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 16.314 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_1_deg 5.6 r_scangle_it 3.552 r_scbond_it 2.445 r_mcangle_it 1.543 r_angle_refined_deg 1.269 r_mcbond_it 0.974 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 16.314 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_1_deg 5.6 r_scangle_it 3.552 r_scbond_it 2.445 r_mcangle_it 1.543 r_angle_refined_deg 1.269 r_mcbond_it 0.974 r_nbtor_refined 0.307 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3069 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing