7JZE

Dihydrodipicolinate synthase mutant S48W with lysine in the allosteric site


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP294.15glucopyranoside, potassium phosphate dibasic
Crystal Properties
Matthews coefficientSolvent content
3.7867.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.162α = 90
b = 121.162β = 90
c = 111.968γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray294.15CCDADSC QUANTUM 315r2011-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95369Australian SynchrotronMX2

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
11.9141.0799.60.07619.311.173748
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)
11.911.950.614

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB entry 1YXC238.3161016325699.610.184070.182040.22264RANDOM32.229
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]
-0.03-0.03-0.030.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.218
r_dihedral_angle_4_deg17.745
r_dihedral_angle_3_deg15.134
r_dihedral_angle_1_deg6.52
r_angle_refined_deg1.97
r_angle_other_deg0.973
r_chiral_restr0.131
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.218
r_dihedral_angle_4_deg17.745
r_dihedral_angle_3_deg15.134
r_dihedral_angle_1_deg6.52
r_angle_refined_deg1.97
r_angle_other_deg0.973
r_chiral_restr0.131
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms4318
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
Aimlessdata scaling
PHASERphasing