3A7U

Crystal structure of the bovine lipoyltransferase in its unliganded form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E5A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPVAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
3.5565.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.175α = 90
b = 91.175β = 90
c = 232.204γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-6040MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9000SPring-8BL44XU

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
13.44501000.0964413.581698169
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)
13.453.511000.4516.514

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 REPLACEMENTTHROUGHOUT2E5A3.4420745260599.370.247790.242240.31839RANDOM73.016
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]
0.310.160.31-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.843
r_dihedral_angle_3_deg16.643
r_dihedral_angle_4_deg12.799
r_dihedral_angle_1_deg5.039
r_scangle_it0.891
r_angle_refined_deg0.863
r_mcangle_it0.704
r_scbond_it0.489
r_mcbond_it0.385
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.843
r_dihedral_angle_3_deg16.643
r_dihedral_angle_4_deg12.799
r_dihedral_angle_1_deg5.039
r_scangle_it0.891
r_angle_refined_deg0.863
r_mcangle_it0.704
r_scbond_it0.489
r_mcbond_it0.385
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 Atoms2600
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling