2ATS

Dihydrodipicolinate synthase co-crystallised with (S)-lysine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP1028420mM Tris HCl, 10mM (S)-lysine, pH 8, 1.8M K2HPO4, pH 10, N-octyl-R-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties
Matthews coefficientSolvent content
3.7567

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.68α = 90
b = 121.68β = 90
c = 109.799γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.933.599.40.0913.82737123320.5
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)
1.91.971000.3423.53.71

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.925.87000236881000.169240.169240.167580.20154RANDOM17.71
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]
-0.43-0.22-0.430.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.974
r_dihedral_angle_4_deg18.834
r_dihedral_angle_3_deg13.292
r_dihedral_angle_1_deg6.007
r_scangle_it3.603
r_scbond_it2.23
r_angle_refined_deg1.395
r_mcangle_it1.166
r_angle_other_deg0.853
r_mcbond_it0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.974
r_dihedral_angle_4_deg18.834
r_dihedral_angle_3_deg13.292
r_dihedral_angle_1_deg6.007
r_scangle_it3.603
r_scbond_it2.23
r_angle_refined_deg1.395
r_mcangle_it1.166
r_angle_other_deg0.853
r_mcbond_it0.63
r_symmetry_hbond_refined0.348
r_symmetry_vdw_other0.263
r_nbd_refined0.235
r_symmetry_vdw_refined0.195
r_nbd_other0.186
r_mcbond_other0.169
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.146
r_metal_ion_refined0.095
r_nbtor_other0.09
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4313
Nucleic Acid Atoms
Solvent Atoms638
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
AMoREphasing