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Human nicotinamide riboside kinase 1 in complex with nicotinamide riboside and an ATP analogue
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 8 291 35% PEG 2000 MME, 0.1M Tris-HCl. The protein solution (40mg/mL) contained 0.01M Nicotinamide riboside, 0.01M AMPPNP and 0.02M Magnesium chloride, pH 8.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.025 α = 90 b = 97.025 β = 90 c = 44.801 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2007-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.92 30 100 0.086 10.7 6.5 31229
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) 1.92 1.99 100 0.999 6.2 3112
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-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 1.92 30 16835 851 99.91 0.211 0.209 0.2127 0.241 0.2442 RANDOM 27.811
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] 0.3 0.3 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.841 r_dihedral_angle_3_deg 13.375 r_dihedral_angle_4_deg 10.315 r_dihedral_angle_1_deg 5.811 r_angle_other_deg 4.146 r_mcangle_it 3.348 r_scangle_it 3.15 r_scbond_it 2.408 r_mcbond_it 2.349 r_angle_refined_deg 1.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.841 r_dihedral_angle_3_deg 13.375 r_dihedral_angle_4_deg 10.315 r_dihedral_angle_1_deg 5.811 r_angle_other_deg 4.146 r_mcangle_it 3.348 r_scangle_it 3.15 r_scbond_it 2.408 r_mcbond_it 2.349 r_angle_refined_deg 1.416 r_symmetry_vdw_refined 0.409 r_symmetry_vdw_other 0.323 r_nbd_other 0.235 r_nbd_refined 0.207 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.161 r_nbtor_other 0.123 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.083 r_bond_refined_d 0.017 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1457 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 50
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction