6J3M

Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Pyrophosphate at 2.30A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ZZC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2981M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6
Crystal Properties
Matthews coefficientSolvent content
5.678.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 216.12α = 90
b = 216.12β = 90
c = 216.12γ = 90
Symmetry
Space GroupF 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2Mmirror2018-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97199ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.376.411000.160.1616.62019784
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)
12.32.381000.85.3

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 REPLACEMENTTHROUGHOUT5ZZC2.376.4118770101099.990.18750.185690.21914RANDOM47.693
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_deg30.085
r_dihedral_angle_4_deg22.409
r_dihedral_angle_3_deg20.675
r_long_range_B_other13.987
r_long_range_B_refined13.963
r_scangle_other11.198
r_mcangle_it8.116
r_mcangle_other8.115
r_scbond_it7.788
r_scbond_other7.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.085
r_dihedral_angle_4_deg22.409
r_dihedral_angle_3_deg20.675
r_long_range_B_other13.987
r_long_range_B_refined13.963
r_scangle_other11.198
r_mcangle_it8.116
r_mcangle_other8.115
r_scbond_it7.788
r_scbond_other7.554
r_dihedral_angle_1_deg7.065
r_mcbond_it5.547
r_mcbond_other5.467
r_angle_refined_deg2.103
r_angle_other_deg1.442
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1305
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing