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Crystal STRUCTURE OF NAMPT IN COMPLEX WITH Compound 11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 1 microliter of protein mixed with 1 microliter of reservoir buffer (27-31% PEG 3350 (w/v), 200 mM NaCl, 100 mM sodium dihydrogen phosphate pH 7.6) incubated for 5 min, then streak seeded (with crystals obtained previously under identical conditions). Ligand added prior to crystallization (2 MILLIMOLAR FROM 100 MILLIMOLAR STOCK IN DMSO) and incubated for 1.5 h at 277 K. CRYO BUFFER consisted of RESERVOIR supplemented WITH 2 MILLIMOLAR INHIBITOR AND 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.207 α = 90 b = 106.26 β = 96.42 c = 120.955 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 PILATUS 6M 2016-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2.33 46.14 97.3 0.228 0.278 0.973 4 2.9 84736 20.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.39 91.1 0.544 0.666 0.617 1.8 2.8
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 2GVJ 2.33 46.14 82564 2100 95.3 0.294 0.2923 0.2942 0.3595 0.3579 RANDOM 18.232
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] -0.17 -0.04 0.39 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.917 r_dihedral_angle_4_deg 19.388 r_dihedral_angle_3_deg 17.649 r_dihedral_angle_1_deg 8.18 r_angle_refined_deg 1.93 r_angle_other_deg 1.316 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.917 r_dihedral_angle_4_deg 19.388 r_dihedral_angle_3_deg 17.649 r_dihedral_angle_1_deg 8.18 r_angle_refined_deg 1.93 r_angle_other_deg 1.316 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14820 Nucleic Acid Atoms Solvent Atoms 1147 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction pointless data scaling PHASER phasing