2CDQ

Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M DI-SODIUM TARTRATE DIHYDRATE, 20 % PEG 3350, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
4.274

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.342α = 90
b = 117.342β = 90
c = 255.283γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2004-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
12.853096.60.0728.33.138693
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)
12.85398.10.441.73

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.8515.673656619361000.2040.2020.244RANDOM62.32
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]
0.550.55-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.433
r_dihedral_angle_3_deg18.169
r_dihedral_angle_4_deg17.876
r_dihedral_angle_1_deg5.556
r_scangle_it1.615
r_angle_refined_deg1.121
r_scbond_it1.082
r_mcangle_it0.766
r_mcbond_it0.514
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.433
r_dihedral_angle_3_deg18.169
r_dihedral_angle_4_deg17.876
r_dihedral_angle_1_deg5.556
r_scangle_it1.615
r_angle_refined_deg1.121
r_scbond_it1.082
r_mcangle_it0.766
r_mcbond_it0.514
r_nbtor_refined0.3
r_nbd_refined0.201
r_symmetry_hbond_refined0.158
r_xyhbond_nbd_refined0.142
r_symmetry_vdw_refined0.138
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7232
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing