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Crystal structure of NAMPT bound to ligand TSY535(compound 9a)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 22% PEG 3350
0.1M NaCl
0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.45 49.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.101 α = 90 b = 108.253 β = 97.16 c = 83.693 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 PIXEL DECTRIS EIGER X 16M 2019-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99999 SLS X06SA
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 2.15 46.99 93.1 0.162 0.197 0.111 0.964 5.8 2.7 54298
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 2.15 2.21 96.8 0.443 0.546 0.314 0.763 2.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GVL 2.15 47.03 51615 2659 92.4 0.2296 0.2277 0.2334 0.2658 0.2717 RANDOM 16.858
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] 3.62 0.16 -2.46 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.695 r_dihedral_angle_4_deg 14.525 r_dihedral_angle_3_deg 13.214 r_dihedral_angle_1_deg 6.464 r_angle_refined_deg 1.19 r_angle_other_deg 1.116 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.695 r_dihedral_angle_4_deg 14.525 r_dihedral_angle_3_deg 13.214 r_dihedral_angle_1_deg 6.464 r_angle_refined_deg 1.19 r_angle_other_deg 1.116 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7365 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 88
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction