☰ Navigation Tabs
Human nicotinamide riboside kinase 1 in complex with nicotinamide riboside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P0E PDB entry 2P0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 15% 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 coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.529 α = 90 b = 141.906 β = 90 c = 62.062 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2007-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.32 40 93.9 0.129 5.4 6.9 54142
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.32 1.37 94.3 0.599 5.4 5348
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2P0E 1.32 36.01 53951 2750 93.59 0.243 0.243 0.242 0.2426 0.26 0.2583 Consistent with isomorphous data set of NRK1.ADP complex 9.765
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.249 r_dihedral_angle_4_deg 15.613 r_dihedral_angle_3_deg 12.044 r_dihedral_angle_1_deg 5.38 r_angle_other_deg 3.998 r_scangle_it 3.043 r_mcangle_it 2.476 r_scbond_it 2.249 r_mcbond_it 1.789 r_angle_refined_deg 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.249 r_dihedral_angle_4_deg 15.613 r_dihedral_angle_3_deg 12.044 r_dihedral_angle_1_deg 5.38 r_angle_other_deg 3.998 r_scangle_it 3.043 r_mcangle_it 2.476 r_scbond_it 2.249 r_mcbond_it 1.789 r_angle_refined_deg 1.48 r_nbd_other 0.229 r_nbd_refined 0.22 r_symmetry_vdw_other 0.2 r_nbtor_refined 0.19 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.146 r_metal_ion_refined 0.12 r_nbtor_other 0.112 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.085 r_bond_refined_d 0.018 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1587 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection PHASER phasing