3K9W

Crystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei with hydrolyzed 3'-dephospho Coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IKZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6289CSHT condition F1: 0.2 M ammonium sulfate, 0.1 M NaOAc pH 4.6, 30% PEG MME 2000, 20% EG as cryo-protectant, 19.2 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% glycerol, 5 mM DTT, crystal tracking ID 204963f1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4349.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.431α = 90
b = 134.431β = 90
c = 134.431γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2009-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97953CLSI08ID-1

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
11.650990.06732.810.727383
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)
11.61.661000.5553.989.1

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 REPLACEMENTTHROUGHOUT3IKZ1.626.3625986136398.890.1920.191190.2069RANDOM15.125
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_deg34.09
r_dihedral_angle_4_deg19.527
r_dihedral_angle_3_deg13.904
r_dihedral_angle_1_deg4.559
r_scangle_it3.115
r_scbond_it1.912
r_mcangle_it1.248
r_angle_refined_deg1.193
r_mcbond_it0.646
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.09
r_dihedral_angle_4_deg19.527
r_dihedral_angle_3_deg13.904
r_dihedral_angle_1_deg4.559
r_scangle_it3.115
r_scbond_it1.912
r_mcangle_it1.248
r_angle_refined_deg1.193
r_mcbond_it0.646
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1279
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms55

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling