2Q7W

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION629825 mM potassium phosphate, 43% saturated ammonium sulfate, 20 mM SADTA, pH 6.0, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9658.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.623α = 90
b = 85.135β = 90
c = 78.849γ = 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
11.477970.06217.45.793239
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)
11.41.4599.80.5712.75.410020

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1AMQ1.476.92293239490396.420.155560.153860.18836RANDOM23.351
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]
-1.030.320.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.75
r_dihedral_angle_4_deg18.82
r_dihedral_angle_3_deg13.056
r_scangle_it5.887
r_dihedral_angle_1_deg5.86
r_scbond_it4.361
r_mcangle_it2.847
r_mcbond_it1.995
r_angle_refined_deg1.923
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.75
r_dihedral_angle_4_deg18.82
r_dihedral_angle_3_deg13.056
r_scangle_it5.887
r_dihedral_angle_1_deg5.86
r_scbond_it4.361
r_mcangle_it2.847
r_mcbond_it1.995
r_angle_refined_deg1.923
r_nbtor_refined0.319
r_nbd_refined0.256
r_symmetry_hbond_refined0.252
r_symmetry_vdw_refined0.234
r_xyhbond_nbd_refined0.218
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2947
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms111

Software

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