2P0E | pdb_00002p0e

Human nicotinamide riboside kinase 1 in complex with tiazofurin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthersame protein in complex with nicotinamide mononucleotide based on an isomorphous crystal

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION929120% PEG 3350, 0.2M Sodium phosphate monobasic, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.550.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.608α = 90
b = 141.571β = 90
c = 62.005γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2007-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418

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
11.82098.90.089117.543446
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)
1.81.860.5267.1

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTsame protein in complex with nicotinamide mononucleotide based on an isomorphous crystal1.819.83822855118198.8970.1760.17450.180.20920.2114.171
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]
0.2890.124-0.413
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.513
r_dihedral_angle_4_deg16.152
r_dihedral_angle_3_deg12.111
r_dihedral_angle_1_deg5.477
r_scangle_it3.571
r_mcangle_it3.109
r_scbond_it2.526
r_mcbond_it2.441
r_angle_refined_deg1.45
r_angle_other_deg0.934
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.513
r_dihedral_angle_4_deg16.152
r_dihedral_angle_3_deg12.111
r_dihedral_angle_1_deg5.477
r_scangle_it3.571
r_mcangle_it3.109
r_scbond_it2.526
r_mcbond_it2.441
r_angle_refined_deg1.45
r_angle_other_deg0.934
r_mcbond_other0.685
r_symmetry_vdw_refined0.214
r_nbd_refined0.209
r_nbd_other0.186
r_nbtor_refined0.179
r_symmetry_hbond_refined0.164
r_symmetry_vdw_other0.159
r_xyhbond_nbd_refined0.138
r_chiral_restr0.09
r_nbtor_other0.084
r_metal_ion_refined0.071
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1581
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms24

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction