3PXU

Crystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei bound to dephospho-coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B6T1B6T molecule A, protein only

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7298Hampton Crystal Screen condition c8, 2.0 M ammonium sulfate, 5.5 mg/mL protein with expression tag removed, crystal tracking ID 203611c8, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6753.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.161α = 90
b = 134.161β = 90
c = 134.161γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
12.0550990.08744.523.213128
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)
12.12.1898.10.5196.5722.41181

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 REPLACEMENTTHROUGHOUT1B6T molecule A, protein only2.128.61228662099.40.20160.19950.2419RANDOM29.9984
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.607
r_dihedral_angle_4_deg17.106
r_dihedral_angle_3_deg14.504
r_dihedral_angle_1_deg5.26
r_scangle_it4.257
r_scbond_it2.584
r_mcangle_it1.549
r_angle_refined_deg1.463
r_mcbond_it0.854
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.607
r_dihedral_angle_4_deg17.106
r_dihedral_angle_3_deg14.504
r_dihedral_angle_1_deg5.26
r_scangle_it4.257
r_scbond_it2.584
r_mcangle_it1.549
r_angle_refined_deg1.463
r_mcbond_it0.854
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1227
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms66

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling