3DKJ

Crystal structure of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DHD	PDB entry 3DHD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	200mM NaCl, 100mM Tris-HCl, 15% PEG 3350, 20% Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.257	α = 90
b = 106.811	β = 96.72
c = 83.045	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	CCD	ADSC QUANTUM 315		2008-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.29000	NSLS	X29A

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	1.9	20	88.6	0.065	6.9	3.8		74005

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)
	1.9	1.97	40.8		0.251		2.6	3402

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3DHD	2	19.92	68540	3452	95.76	0.17	0.168	0.209	RANDOM	24.413

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]
-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.754
r_dihedral_angle_4_deg	15.253
r_dihedral_angle_3_deg	14.311
r_dihedral_angle_1_deg	5.984
r_scangle_it	3.44
r_scbond_it	2.177
r_angle_refined_deg	1.498
r_mcangle_it	1.267
r_mcbond_it	0.806
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.754
r_dihedral_angle_4_deg	15.253
r_dihedral_angle_3_deg	14.311
r_dihedral_angle_1_deg	5.984
r_scangle_it	3.44
r_scbond_it	2.177
r_angle_refined_deg	1.498
r_mcangle_it	1.267
r_mcbond_it	0.806
r_nbtor_refined	0.305
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7450
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	62

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.