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CRYSTAL STRUCTURE OF NAMPT IN COMPLEX WITH COMPOUND 9
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 15% ETHYLENGLYCOL
Crystal Properties Matthews coefficient Solvent content 2.39 48.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.956 α = 90 b = 106.18 β = 96.53 c = 121.34 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 2014-08-28 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 2.13 48.59 98 0.121 0.151 0.994 6.89 2.67 114934 24.9
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 2.13 2.26 96.1 0.459 0.57 0.854 2.2 2.7
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 2.13 48.59 109187 5747 97.97 0.2553 0.2528 0.2591 0.3025 0.3066 RANDOM 20.514
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] -0.76 -0.65 -0.2 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.735 r_dihedral_angle_4_deg 16.37 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 6.907 r_angle_refined_deg 1.422 r_angle_other_deg 1.286 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.735 r_dihedral_angle_4_deg 16.37 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 6.907 r_angle_refined_deg 1.422 r_angle_other_deg 1.286 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14937 Nucleic Acid Atoms Solvent Atoms 1329 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction pointless data scaling PHASER phasing