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Crystal Structure of human NAMPT in complex with NVP-LOD812
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 18 % (v/v) glycerol
23 % (w/v) PEG 3350
200 mM NaCl
100 mM Tris/HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.23 44.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.46 α = 90 b = 208.4 β = 90 c = 98.86 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 2013-02-14 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 2.53 207.99 99.8 0.142 8.6 6 77346 44.89
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 2.53 2.67 99.9 0.476 3.2 5.9
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 3DGR 2.53 104.2 77346 3492 99.96 0.1555 0.1523 0.1508 0.2147 0.2108 RANDOM 39.24
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] 7.3066 -9.9568 2.6502
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.92 t_omega_torsion 3.13 t_angle_deg 1.16 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 18.92 t_omega_torsion 3.13 t_angle_deg 1.16 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 14966 Nucleic Acid Atoms Solvent Atoms 1123 Heterogen Atoms 1293
Software Software Software Name Purpose XDS data reduction SCALA data scaling BUSTER phasing BUSTER refinement