9IYH

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.25 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
2.7154.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.925α = 90
b = 78.622β = 93.118
c = 106.985γ = 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)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
12.2542.66896.30.1340.1330.984.62.152114
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)
12.252.320.7220.7210.4451.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.2542.66852073105795.7450.2260.2250.230.25130.2642.291
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]
1.3010.5071.116-2.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.214
r_dihedral_angle_3_deg13.215
r_lrange_other11.561
r_lrange_it11.56
r_dihedral_angle_2_deg8.784
r_scangle_it6.846
r_scangle_other6.846
r_dihedral_angle_1_deg5.879
r_mcangle_it5.8
r_mcangle_other5.8
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7662
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms68

Software

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