2QA3

Structural Studies Reveal the Inactivation of E. coli L-aspartate aminotransferase by (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) via two mechanisms (at pH6.5)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AMQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.5298The well solutions contained 25 mM potassium phosphate and 43% saturated ammonium sulfate with 20 mM of SADTA at pH 6.5, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9458.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.897α = 90
b = 84.9β = 90
c = 78.877γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.752799.60.06510.8751173
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.811000.5663.36.95050

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1AMQ1.7576.923.349413265699.580.15650.154380.19706RANDOM22.107
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]
-1.130.450.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.826
r_dihedral_angle_4_deg20.883
r_dihedral_angle_3_deg14.248
r_dihedral_angle_1_deg5.616
r_scangle_it3.701
r_scbond_it2.61
r_mcangle_it1.584
r_angle_refined_deg1.425
r_mcbond_it1.011
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.826
r_dihedral_angle_4_deg20.883
r_dihedral_angle_3_deg14.248
r_dihedral_angle_1_deg5.616
r_scangle_it3.701
r_scbond_it2.61
r_mcangle_it1.584
r_angle_refined_deg1.425
r_mcbond_it1.011
r_nbtor_refined0.307
r_nbd_refined0.23
r_symmetry_vdw_refined0.197
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.15
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2994
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms133

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing