2QB2

Structural Studies Reveal the Inactivation of E. coli L-aspartate aminotransferase by (s)-4,5-dihydro-2thiophenecarboylic acid (SADTA) via two mechanisms (at pH 7.0).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7298The well solutions contained 25 mM potassium phosphate and 43% saturated ammonium sulfate with 20 mM of SADTA at pH 7.0, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9458.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.91α = 90
b = 84.684β = 90
c = 78.865γ = 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
11.72796.10.05713.74.554569
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)
11.71.7696.60.5252.64.15425

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 REPLACEMENTTHROUGHOUT1AMQ1.7272.654569289296.120.146730.144720.18419RANDOM22.314
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]
-1.10.840.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.872
r_dihedral_angle_4_deg20.111
r_dihedral_angle_3_deg14.562
r_dihedral_angle_1_deg5.795
r_scangle_it5.7
r_scbond_it4.21
r_mcangle_it2.611
r_angle_refined_deg1.832
r_mcbond_it1.811
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.872
r_dihedral_angle_4_deg20.111
r_dihedral_angle_3_deg14.562
r_dihedral_angle_1_deg5.795
r_scangle_it5.7
r_scbond_it4.21
r_mcangle_it2.611
r_angle_refined_deg1.832
r_mcbond_it1.811
r_nbtor_refined0.316
r_nbd_refined0.25
r_symmetry_vdw_refined0.228
r_symmetry_hbond_refined0.203
r_xyhbond_nbd_refined0.18
r_chiral_restr0.122
r_bond_refined_d0.019
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2986
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms122

Software

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