2H3D

Crystal Structure of Mouse Nicotinamide Phosphoribosyltransferase/Visfatin/Pre-B Cell Colony Enhancing Factor in Complex with Nicotinamide Mononuleotide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.82915 mg/ml Se-Met Nampt with 10 mM added NMN and reservoir solution containing 0.1 M HEPES pH 7.8, 0.1 M Na acetate, and 14.5% PEG4000 in a 1:1 ratio in a total initial drop volume of 2 microliter., VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.80
Crystal Properties
Matthews coefficientSolvent content
2.4449.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.46α = 90
b = 107.96β = 96.98
c = 83.65γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCD2005-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.15098.90.10613.43.26107317.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1892.60.3322.72.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.140.1361048304398.60.2150.2150.238RANDOM28.4
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]
8.77-7.19-3.39-5.38
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.4
c_scangle_it2.98
c_scbond_it2.08
c_mcangle_it1.82
c_mcbond_it1.23
c_angle_deg1.2
c_improper_angle_d0.77
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7431
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms44

Software

Software
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing