6PBR

Catalytic domain of E.coli dihydrolipoamide succinyltransferase in I4 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C4T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829850 mM Tris pH 8.0 2.6 M NaCl
Crystal Properties
Matthews coefficientSolvent content
3.3363

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.598α = 90
b = 128.598β = 90
c = 249.733γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.92NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
1347.3682.90.220.1250.983.73.73357060.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1685.51.470.860.340.83.6

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 REPLACEMENTTHROUGHOUT1C4T347.3631857164182.830.23240.230310.27172RANDOM76.611
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]
0.070.07-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.376
r_dihedral_angle_4_deg16.243
r_dihedral_angle_3_deg15.417
r_long_range_B_refined12.444
r_long_range_B_other12.443
r_mcangle_it9.055
r_mcangle_other9.055
r_scangle_other7.925
r_dihedral_angle_1_deg5.951
r_mcbond_it5.711
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.376
r_dihedral_angle_4_deg16.243
r_dihedral_angle_3_deg15.417
r_long_range_B_refined12.444
r_long_range_B_other12.443
r_mcangle_it9.055
r_mcangle_other9.055
r_scangle_other7.925
r_dihedral_angle_1_deg5.951
r_mcbond_it5.711
r_mcbond_other5.711
r_scbond_it4.823
r_scbond_other4.823
r_angle_refined_deg1.539
r_angle_other_deg1.043
r_chiral_restr0.051
r_bond_refined_d0.007
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 Atoms10962
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
SIMBADphasing