3EI8

Crystal structure of K270N variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with LL-DAP: External aldimine form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z20PDB entry 2Z20

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529845% (NH4)2SO4, 0.1 M HEPES pH 7.5, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7455.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.476α = 90
b = 102.476β = 90
c = 171.68γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.115872ALS8.3.1

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
11.64099.80.073137740137740
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)
11.61.6699.20.644

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 REPLACEMENTTHROUGHOUTPDB entry 2Z201.639.41130739130739692199.770.168190.167170.18769RANDOM22.445
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]
-0.52-0.26-0.520.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.066
r_dihedral_angle_4_deg19.884
r_dihedral_angle_3_deg12.853
r_dihedral_angle_1_deg5.359
r_scangle_it3.437
r_scbond_it2.077
r_angle_refined_deg1.222
r_mcangle_it1.214
r_mcbond_it0.609
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.066
r_dihedral_angle_4_deg19.884
r_dihedral_angle_3_deg12.853
r_dihedral_angle_1_deg5.359
r_scangle_it3.437
r_scbond_it2.077
r_angle_refined_deg1.222
r_mcangle_it1.214
r_mcbond_it0.609
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6346
Nucleic Acid Atoms
Solvent Atoms1016
Heterogen Atoms89

Software

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