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Human nicotinamide riboside kinase 1 in complex with tiazofurin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other same protein in complex with nicotinamide mononucleotide based on an isomorphous crystal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 291 20% PEG 3350, 0.2M Sodium phosphate monobasic, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 50.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.608 α = 90 b = 141.571 β = 90 c = 62.005 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 2007-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 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 1.8 20 98.9 0.089 11 7.5 43446
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) 1.8 1.86 0.526 7.1
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT same protein in complex with nicotinamide mononucleotide based on an isomorphous crystal 1.8 19.838 22855 1181 98.897 0.176 0.1745 0.1798 0.2092 0.2116 14.171
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] 0.289 0.124 -0.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.513 r_dihedral_angle_4_deg 16.152 r_dihedral_angle_3_deg 12.111 r_dihedral_angle_1_deg 5.477 r_scangle_it 3.571 r_mcangle_it 3.109 r_scbond_it 2.526 r_mcbond_it 2.441 r_angle_refined_deg 1.45 r_angle_other_deg 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.513 r_dihedral_angle_4_deg 16.152 r_dihedral_angle_3_deg 12.111 r_dihedral_angle_1_deg 5.477 r_scangle_it 3.571 r_mcangle_it 3.109 r_scbond_it 2.526 r_mcbond_it 2.441 r_angle_refined_deg 1.45 r_angle_other_deg 0.934 r_mcbond_other 0.685 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.209 r_nbd_other 0.186 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.164 r_symmetry_vdw_other 0.159 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.09 r_nbtor_other 0.084 r_metal_ion_refined 0.071 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1581 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction