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Human nicotinamide riboside kinase 1 in complex with ADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 20% PEG 3350, 0.2M Sodium phosphate monobasic, 0.15M D(+)sucrose, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.453 α = 90 b = 142.07 β = 90 c = 62.263 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 2006-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.97931 APS 17-ID
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 1.9 50 99.6 0.122 6.4 6.9 19430
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) 1.9 1.97 96.6 0.709 5.4 1857
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.95 28.51 17990 933 99.78 0.222 0.222 0.219 0.2243 0.263 0.2635 RANDOM 18.786
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] 0.25 -0.04 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.986 r_dihedral_angle_4_deg 17.76 r_dihedral_angle_3_deg 13.731 r_dihedral_angle_1_deg 5.479 r_angle_other_deg 4.148 r_mcangle_it 3.562 r_scangle_it 3.409 r_scbond_it 2.604 r_mcbond_it 2.531 r_angle_refined_deg 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.986 r_dihedral_angle_4_deg 17.76 r_dihedral_angle_3_deg 13.731 r_dihedral_angle_1_deg 5.479 r_angle_other_deg 4.148 r_mcangle_it 3.562 r_scangle_it 3.409 r_scbond_it 2.604 r_mcbond_it 2.531 r_angle_refined_deg 1.46 r_nbd_other 0.229 r_symmetry_vdw_other 0.21 r_nbd_refined 0.203 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.149 r_nbtor_other 0.108 r_chiral_restr 0.082 r_bond_refined_d 0.016 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_metal_ion_refined r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1480 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction