3EI7

Crystal structure of apo-LL-diaminopimelate aminotransferase from Arabidopsis thaliana (no PLP)


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
2.7755.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.101α = 90
b = 103.101β = 90
c = 171.827γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-06-27MSINGLE 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
11.99401000.0787301373013
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)
1.992.061000.797

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 2Z201.9938.726925669256368099.90.191250.189210.2293RANDOM36.888
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]
-0.77-0.38-0.771.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.821
r_dihedral_angle_4_deg16.327
r_dihedral_angle_3_deg15.746
r_dihedral_angle_1_deg6.333
r_scangle_it4.57
r_scbond_it2.859
r_mcangle_it2.066
r_angle_refined_deg1.551
r_mcbond_it1.127
r_chiral_restr0.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.821
r_dihedral_angle_4_deg16.327
r_dihedral_angle_3_deg15.746
r_dihedral_angle_1_deg6.333
r_scangle_it4.57
r_scbond_it2.859
r_mcangle_it2.066
r_angle_refined_deg1.551
r_mcbond_it1.127
r_chiral_restr0.121
r_bond_refined_d0.018
r_gen_planes_refined0.008
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 Atoms6338
Nucleic Acid Atoms
Solvent Atoms629
Heterogen Atoms10

Software

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