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Human NAMPT in complex with substrate NAM and small molecule activator ZN-29-S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 0.1 M Tris-HCl, pH 8.5, 0.2M NaCl, 20% glycerol and 13-18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.888 α = 90 b = 106.997 β = 96.88 c = 83.603 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX-300 2019-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.2 65.58 99.9 0.113 0.132 0.068 0.989 6.8 3.7 53951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 98.7 0.396 0.478 0.263 0.867 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 65.58 1.34 53886 2614 99.8 0.2279 0.2261 0.229 0.2642 0.267
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.492 f_angle_d 0.977 f_chiral_restr 0.077 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7482 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 101
Software Software Software Name Purpose DIALS data reduction Aimless data scaling MOLREP phasing PHENIX refinement