7LOY

Dihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I7UPDB entry 4I7U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1520% w/v PEG3000, 0.1 M sodium citrate, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.7254.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.777α = 90
b = 133.581β = 100.55
c = 155.988γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS EIGER X 16M2018-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953723Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.446.3299.820.9171.04479992
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4860.702

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 4I7U2.446.2775861405099.870.203130.200540.25191RANDOM35.948
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]
0.05-0.05-0.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.494
r_dihedral_angle_4_deg19.919
r_dihedral_angle_3_deg14.245
r_dihedral_angle_1_deg7.16
r_long_range_B_refined5.119
r_long_range_B_other5.119
r_scangle_other3.701
r_mcangle_it3.142
r_mcangle_other3.142
r_scbond_it2.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.494
r_dihedral_angle_4_deg19.919
r_dihedral_angle_3_deg14.245
r_dihedral_angle_1_deg7.16
r_long_range_B_refined5.119
r_long_range_B_other5.119
r_scangle_other3.701
r_mcangle_it3.142
r_mcangle_other3.142
r_scbond_it2.333
r_scbond_other2.331
r_mcbond_it2.045
r_mcbond_other2.045
r_angle_refined_deg1.428
r_angle_other_deg1.217
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13416
Nucleic Acid Atoms
Solvent Atoms448
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
pointlessdata scaling
PHASERphasing
XDSdata reduction