9IYF

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.37 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
2.6854.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.268α = 90
b = 78.418β = 93.1
c = 106.465γ = 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
12.3742.48694.90.2330.2330.9642.62.143453
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)
12.372.4697.41.2351.2340.340.82.1

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-VALUE2.3742.4864345386394.3770.220.21970.246444.031
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]
1.8570.1330.74-2.596
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.875
r_dihedral_angle_6_deg14.499
r_dihedral_angle_3_deg13.527
r_lrange_other11.447
r_lrange_it11.445
r_dihedral_angle_1_deg5.956
r_scangle_it5.855
r_scangle_other5.854
r_mcangle_it5.355
r_mcangle_other5.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.875
r_dihedral_angle_6_deg14.499
r_dihedral_angle_3_deg13.527
r_lrange_other11.447
r_lrange_it11.445
r_dihedral_angle_1_deg5.956
r_scangle_it5.855
r_scangle_other5.854
r_mcangle_it5.355
r_mcangle_other5.355
r_scbond_it3.444
r_scbond_other3.444
r_mcbond_it3.207
r_mcbond_other3.207
r_angle_refined_deg1.317
r_angle_other_deg0.72
r_nbd_other0.245
r_symmetry_xyhbond_nbd_refined0.23
r_symmetry_nbd_other0.209
r_nbd_refined0.198
r_symmetry_nbd_refined0.194
r_xyhbond_nbd_refined0.187
r_nbtor_refined0.173
r_ncsr_local_group_100.146
r_ncsr_local_group_20.139
r_ncsr_local_group_110.138
r_ncsr_local_group_60.131
r_ncsr_local_group_120.131
r_ncsr_local_group_130.128
r_ncsr_local_group_30.116
r_ncsr_local_group_150.116
r_ncsr_local_group_80.114
r_ncsr_local_group_70.107
r_ncsr_local_group_140.107
r_ncsr_local_group_10.106
r_ncsr_local_group_50.106
r_ncsr_local_group_90.09
r_ncsr_local_group_40.087
r_symmetry_nbtor_other0.082
r_xyhbond_nbd_other0.069
r_chiral_restr0.064
r_symmetry_xyhbond_nbd_other0.053
r_gen_planes_other0.008
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7662
Nucleic Acid Atoms
Solvent Atoms573
Heterogen Atoms68

Software

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