3PA9

Mechanism of inactivation of E. coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA) pH 7.5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5297Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.9958.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.135α = 90
b = 85.532β = 90
c = 79.033γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.97APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.777.297.767102

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 1AMQ1.777.1526710253395285197.830.150120.148270.18519RANDOM23.043
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]
-0.590.550.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg16.314
r_dihedral_angle_3_deg13.484
r_dihedral_angle_1_deg5.6
r_scangle_it3.552
r_scbond_it2.445
r_mcangle_it1.543
r_angle_refined_deg1.269
r_mcbond_it0.974
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg16.314
r_dihedral_angle_3_deg13.484
r_dihedral_angle_1_deg5.6
r_scangle_it3.552
r_scbond_it2.445
r_mcangle_it1.543
r_angle_refined_deg1.269
r_mcbond_it0.974
r_nbtor_refined0.307
r_nbd_refined0.22
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.121
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3069
Nucleic Acid Atoms
Solvent Atoms420
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing