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Human nicotinamide riboside kinase 1 in complex with nicotinamide mononucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QSY PDB entry 2QSY
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 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.921 α = 90 b = 142.342 β = 90 c = 62.434 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 IMAGE PLATE RIGAKU RAXIS 2007-01-26 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 1.9 30 99.1 0.138 6.4 4.8 19738
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 98.1 0.901 4.2 1906
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 2QSY 1.9 23.64 19721 1031 98.63 0.219 0.217 0.2235 0.255 0.2576 Reflections from isomorphous data of NRK1-ADP complex 21.061
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] 0.03 0.28 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.625 r_dihedral_angle_4_deg 18.199 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 5.757 r_angle_other_deg 4.119 r_scangle_it 2.905 r_mcangle_it 2.84 r_scbond_it 2.156 r_mcbond_it 2.069 r_angle_refined_deg 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.625 r_dihedral_angle_4_deg 18.199 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 5.757 r_angle_other_deg 4.119 r_scangle_it 2.905 r_mcangle_it 2.84 r_scbond_it 2.156 r_mcbond_it 2.069 r_angle_refined_deg 1.323 r_nbd_other 0.228 r_nbd_refined 0.196 r_nbtor_refined 0.177 r_symmetry_vdw_other 0.168 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.117 r_nbtor_other 0.108 r_chiral_restr 0.079 r_bond_refined_d 0.015 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1559 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 35
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing