2QT1

Human nicotinamide riboside kinase 1 in complex with nicotinamide riboside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P0EPDB entry 2P0E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION629115% PEG 3350, 0.2M Sodium phosphate monobasic, 0.1M Bis-Tris. The protein solution (40mg/mL) contained 0.01M Nicotinamide riboside, 0.01M AMPPNP and 0.02M Magnesium chloride, pH 6.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5150.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.529α = 90
b = 141.906β = 90
c = 62.062γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2007-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97934APS23-ID-D

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
11.324093.90.1295.46.954142
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)
1.321.3794.30.5995.45348

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2P0E1.3236.0153951275093.590.2430.2430.2420.26Consistent with isomorphous data set of NRK1.ADP complex9.765
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]
0.17-0.13-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.249
r_dihedral_angle_4_deg15.613
r_dihedral_angle_3_deg12.044
r_dihedral_angle_1_deg5.38
r_angle_other_deg3.998
r_scangle_it3.043
r_mcangle_it2.476
r_scbond_it2.249
r_mcbond_it1.789
r_angle_refined_deg1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.249
r_dihedral_angle_4_deg15.613
r_dihedral_angle_3_deg12.044
r_dihedral_angle_1_deg5.38
r_angle_other_deg3.998
r_scangle_it3.043
r_mcangle_it2.476
r_scbond_it2.249
r_mcbond_it1.789
r_angle_refined_deg1.48
r_nbd_other0.229
r_nbd_refined0.22
r_symmetry_vdw_other0.2
r_nbtor_refined0.19
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.146
r_metal_ion_refined0.12
r_nbtor_other0.112
r_symmetry_hbond_refined0.11
r_chiral_restr0.085
r_bond_refined_d0.018
r_gen_planes_other0.011
r_gen_planes_refined0.008
r_bond_other_d
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1587
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms30

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
PHASERphasing