8I8J

Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Coenzyme-A and Phosphonoacetic acid at 2.07 A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8I8I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.754.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.966α = 90
b = 78.659β = 93.121
c = 107.027γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2022-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8731ESRFID23-2

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
12.0741.5596.80.9893.12.16861544.9
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)
12.072.130.182

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.0741.54667601101496.8370.2260.22540.276651.94
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]
0.003-0.001-0.002-0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.744
r_dihedral_angle_6_deg14.408
r_lrange_it9.696
r_lrange_other9.692
r_dihedral_angle_2_deg9.2
r_dihedral_angle_1_deg6.838
r_scangle_it6.777
r_scangle_other6.776
r_mcangle_it5.648
r_mcangle_other5.647
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.744
r_dihedral_angle_6_deg14.408
r_lrange_it9.696
r_lrange_other9.692
r_dihedral_angle_2_deg9.2
r_dihedral_angle_1_deg6.838
r_scangle_it6.777
r_scangle_other6.776
r_mcangle_it5.648
r_mcangle_other5.647
r_scbond_it4.278
r_scbond_other4.277
r_mcbond_it3.632
r_mcbond_other3.632
r_angle_refined_deg1.253
r_angle_other_deg0.689
r_dihedral_angle_other_2_deg0.545
r_nbd_other0.237
r_nbd_refined0.219
r_symmetry_nbd_other0.219
r_symmetry_nbd_refined0.214
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.179
r_symmetry_xyhbond_nbd_refined0.177
r_symmetry_nbtor_other0.082
r_chiral_restr0.056
r_symmetry_xyhbond_nbd_other0.051
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7547
Nucleic Acid Atoms
Solvent Atoms437
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building