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Crystal Structure of human NAMPT in complex with NVP-LVR596
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ATB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 25 % (w/v) PEG 3350,
200 mM NaCl,
100 mM Tris/HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.87 α = 90 b = 96.83 β = 90 c = 248.3 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2013-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.44 248.3 100 0.065 18.4 6.6 81287 61.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.57 100 0.582 2.6 6.6 11185
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 FOURIER SYNTHESIS THROUGHOUT 6atb 2.44 124.15 81198 4070 99.68 0.1814 0.1787 0.1844 0.2327 0.2417 RANDOM 58.39
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] 3.3529 -15.3302 11.9774
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.47 t_omega_torsion 3.01 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.47 t_omega_torsion 3.01 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15028 Nucleic Acid Atoms Solvent Atoms 876 Heterogen Atoms 1031
Software Software Software Name Purpose XDS data reduction SCALA data scaling BUSTER refinement BUSTER phasing