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Human NAMPT in complex with substrate NAM and small molecule activator NP-A3
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, 0.2 M NaCl, 20% glycerol and 13-18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.56 α = 90 b = 106.864 β = 96.71 c = 83.222 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 2019-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 1.79 52.47 99.8 0.087 0.102 0.053 0.996 8.7 3.6 98774
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 1.79 1.82 97.3 0.755 0.991 0.636 0.594 2.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2e5d 1.79 52.47 93639 5055 99.78 0.17887 0.17783 0.19753 0.1974 RANDOM 18.233
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] 1.41 -0.41 -0.01 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.744 r_dihedral_angle_3_deg 11.951 r_dihedral_angle_4_deg 10.591 r_dihedral_angle_1_deg 6.757 r_long_range_B_refined 3.785 r_long_range_B_other 3.732 r_scangle_other 2.852 r_scbond_it 1.819 r_scbond_other 1.819 r_mcangle_it 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.744 r_dihedral_angle_3_deg 11.951 r_dihedral_angle_4_deg 10.591 r_dihedral_angle_1_deg 6.757 r_long_range_B_refined 3.785 r_long_range_B_other 3.732 r_scangle_other 2.852 r_scbond_it 1.819 r_scbond_other 1.819 r_mcangle_it 1.69 r_mcangle_other 1.69 r_angle_refined_deg 1.365 r_angle_other_deg 1.318 r_mcbond_it 1.11 r_mcbond_other 1.109 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7450 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 103
Software Software Software Name Purpose DIALS data reduction Aimless data scaling MOLREP phasing REFMAC refinement