5YOL

Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4S0M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298HEPES: 7.5, PEG400, 0.1MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.5351.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.1α = 80.51
b = 69.93β = 69.94
c = 71.7γ = 89.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6Mmirror2017-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.96600ESRFID29

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
12.266.32289.30.0518.91.756966
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)
12.22.23989.10.3752.1

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 REPLACEMENTTHROUGHOUT4S0M2.266.32254227273989.240.215020.212810.2576RANDOM43.307
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]
-0.69-0.090.86-0.90.341.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.975
r_dihedral_angle_4_deg19.309
r_dihedral_angle_3_deg16.15
r_long_range_B_refined9.664
r_long_range_B_other9.643
r_scangle_other6.955
r_dihedral_angle_1_deg5.978
r_mcangle_it5.162
r_mcangle_other5.162
r_scbond_it4.472
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.975
r_dihedral_angle_4_deg19.309
r_dihedral_angle_3_deg16.15
r_long_range_B_refined9.664
r_long_range_B_other9.643
r_scangle_other6.955
r_dihedral_angle_1_deg5.978
r_mcangle_it5.162
r_mcangle_other5.162
r_scbond_it4.472
r_scbond_other4.472
r_mcbond_it3.463
r_mcbond_other3.462
r_angle_refined_deg1.624
r_angle_other_deg1.014
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms8704
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing