3I7S

Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound in the active site.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YXC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP102761.8M POTASSIUM PHOSPHATE, PH 10, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 276K
Crystal Properties
Matthews coefficientSolvent content
3.7266.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.881α = 90
b = 120.881β = 90
c = 110.5γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV2007-10-10MSINGLE 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)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
12.332.17950.0880.0887.43.42398303983022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3897.30.350.352.83.27

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 REPLACEMENTTHROUGHOUT1yxc2.332.173780237802201994.970.197840.195820.23582RANDOM27.751
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]
-0.12-0.06-0.120.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.693
r_dihedral_angle_4_deg17.417
r_dihedral_angle_3_deg15.394
r_dihedral_angle_1_deg6.131
r_scangle_it3.312
r_scbond_it2.013
r_angle_refined_deg1.364
r_mcangle_it1.086
r_mcbond_it0.561
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.693
r_dihedral_angle_4_deg17.417
r_dihedral_angle_3_deg15.394
r_dihedral_angle_1_deg6.131
r_scangle_it3.312
r_scbond_it2.013
r_angle_refined_deg1.364
r_mcangle_it1.086
r_mcbond_it0.561
r_chiral_restr0.091
r_bond_refined_d0.012
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 Atoms4360
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms81

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling