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Crystal structure of human nicotinamide riboside kinase (NRK1) in complex with nicotinamide mononucleotide (NMN)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 28% (w/v) PEG 3350, 200 mM NH4Cl, 5 mM DTT, 5 mM Na2HPO, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.725 α = 90 b = 141.526 β = 90 c = 62.091 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 ADSC QUANTUM 4 2006-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97935 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 30 99.5 0.087 23.3 6.1 75133 74763 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.55 98.2 0.462 2.77 3.9 7396
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION SAD 1.5 30 71557 71557 5386 95.9 0.191 0.206 0.191 0.2051 0.206 0.2163 19.163
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] -2.563 2.032 0.531
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.197 c_scbond_it 2.146 c_mcangle_it 1.919 c_angle_d 1.259 c_mcbond_it 1.172 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 27
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling SOLVE phasing