8TM7

Human NAMPT in complex with substrate NAM and small molecule activator NP-A3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E5D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52900.1 M Tris-HCl, pH 8.5, 0.2 M NaCl, 20% glycerol and 13-18% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3647.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.56α = 90
b = 106.864β = 96.71
c = 83.222γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002019-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7952.4799.80.0870.1020.0530.9968.73.698774
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.8297.30.7550.9910.6360.5942.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2e5d1.7952.4793639505599.780.178870.177830.19753RANDOM18.233
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]
1.41-0.41-0.01-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.744
r_dihedral_angle_3_deg11.951
r_dihedral_angle_4_deg10.591
r_dihedral_angle_1_deg6.757
r_long_range_B_refined3.785
r_long_range_B_other3.732
r_scangle_other2.852
r_scbond_it1.819
r_scbond_other1.819
r_mcangle_it1.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.744
r_dihedral_angle_3_deg11.951
r_dihedral_angle_4_deg10.591
r_dihedral_angle_1_deg6.757
r_long_range_B_refined3.785
r_long_range_B_other3.732
r_scangle_other2.852
r_scbond_it1.819
r_scbond_other1.819
r_mcangle_it1.69
r_mcangle_other1.69
r_angle_refined_deg1.365
r_angle_other_deg1.318
r_mcbond_it1.11
r_mcbond_other1.109
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7450
Nucleic Acid Atoms
Solvent Atoms435
Heterogen Atoms103

Software

Software
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement