5I0C

Crystal structure of predicted acyltransferase YjdJ with acyl-CoA N-acyltransferase domain from Escherichia coli str. K-12


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M HEPES, 5 mM Cobalt Chloride, 5 mM Magnesium Chloride, 0.5 mM Cadmium Chloride, 0.5 mM Nickel Chloride, 12 % (w/v) PEG3350, 25 Sucrose, 1 mM AcCoA
Crystal Properties
Matthews coefficientSolvent content
2.2846.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.69α = 90
b = 87.84β = 90
c = 41.58γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

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
11.9230.1998.90.03827.97.17731
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)
11.921.9799.60.592.97.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.9230.19734435498.340.217820.215510.26595RANDOM44.871
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]
-1.73.13-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.668
r_sphericity_bonded41.565
r_dihedral_angle_4_deg21.283
r_dihedral_angle_3_deg19.694
r_dihedral_angle_1_deg8.739
r_long_range_B_refined6.662
r_long_range_B_other6.539
r_scangle_other3.552
r_mcangle_other3.515
r_mcangle_it3.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.668
r_sphericity_bonded41.565
r_dihedral_angle_4_deg21.283
r_dihedral_angle_3_deg19.694
r_dihedral_angle_1_deg8.739
r_long_range_B_refined6.662
r_long_range_B_other6.539
r_scangle_other3.552
r_mcangle_other3.515
r_mcangle_it3.514
r_scbond_it2.401
r_mcbond_it2.386
r_mcbond_other2.361
r_scbond_other2.327
r_angle_refined_deg2.223
r_angle_other_deg1.18
r_chiral_restr0.147
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms723
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHENIXphasing
PHENIXmodel building
XDSdata reduction