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Crystal structure of human NAMPT with A-1326133
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 277 25% PEG 3350, 0.2 M ammonium sulfate, and 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.166 α = 90 b = 107.049 β = 96.77 c = 83.135 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 2011-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.73 107 97.9 15 3.2 109253 25.25
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 1.73 25.33 108403 5439 98 0.165 0.164 0.1662 0.192 0.1965 RANDOM 27.67
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] -3.122 0.369 -4.4911 7.6131
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.89 t_omega_torsion 3.76 t_angle_deg 1.04 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.89 t_omega_torsion 3.76 t_angle_deg 1.04 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 7431 Nucleic Acid Atoms Solvent Atoms 836 Heterogen Atoms 88
Software Software Software Name Purpose SCALA data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing