3V7Y

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-N-Propargylamino-5'-deoxyadenosine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5291.1530 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
2.2745.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.812α = 90
b = 75.675β = 90
c = 118.619γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.979338ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9748.3499.94.820293
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.0899.9

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONIsomorphous replacement1.9748.3321.062029360394.830.19440.19340.2292
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]
1.62368.6491-10.2727
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.949
f_angle_d0.925
f_chiral_restr0.064
f_bond_d0.009
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2054
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms57

Software

Software
Software NamePurpose
ADSCdata collection
PHENIXrefinement
XDSdata reduction
SCALAdata scaling