2Z1Z

Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana complexed with L-malate ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNative LL-diaminopimelate aminotransferase structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982.1M D,L-malic acid, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.7655.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.587α = 90
b = 102.587β = 90
c = 172.939γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210KOHZU: Double Crystal Si(111)2006-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11590ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.42090.40.08313.543783137831
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4993.60.5531.93.73838

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTNative LL-diaminopimelate aminotransferase structure2.4203589635896191690.160.183090.179560.25073RANDOM36.565
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]
-1.16-0.58-1.161.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.465
r_dihedral_angle_4_deg21.553
r_dihedral_angle_3_deg21.136
r_dihedral_angle_1_deg8.548
r_scangle_it4.824
r_scbond_it3.33
r_angle_refined_deg2.374
r_mcangle_it2.08
r_mcbond_it1.259
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.465
r_dihedral_angle_4_deg21.553
r_dihedral_angle_3_deg21.136
r_dihedral_angle_1_deg8.548
r_scangle_it4.824
r_scbond_it3.33
r_angle_refined_deg2.374
r_mcangle_it2.08
r_mcbond_it1.259
r_nbtor_refined0.318
r_symmetry_hbond_refined0.271
r_nbd_refined0.245
r_symmetry_vdw_refined0.233
r_xyhbond_nbd_refined0.176
r_chiral_restr0.173
r_bond_refined_d0.028
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6288
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing