2QT1

Human nicotinamide riboside kinase 1 in complex with nicotinamide riboside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P0E	PDB entry 2P0E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	291	15% PEG 3350, 0.2M Sodium phosphate monobasic, 0.1M Bis-Tris. The protein solution (40mg/mL) contained 0.01M Nicotinamide riboside, 0.01M AMPPNP and 0.02M Magnesium chloride, pH 6.0, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.529	α = 90
b = 141.906	β = 90
c = 62.062	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	MARMOSAIC 325 mm CCD		2007-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97934	APS	23-ID-D

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	1.32	40	93.9	0.129	5.4	6.9		54142

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)
	1.32	1.37	94.3		0.599		5.4	5348

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2P0E	1.32	36.01	53951	2750	93.59	0.243	0.243	0.242	0.26	Consistent with isomorphous data set of NRK1.ADP complex	9.765

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]
0.17			-0.13		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.249
r_dihedral_angle_4_deg	15.613
r_dihedral_angle_3_deg	12.044
r_dihedral_angle_1_deg	5.38
r_angle_other_deg	3.998
r_scangle_it	3.043
r_mcangle_it	2.476
r_scbond_it	2.249
r_mcbond_it	1.789
r_angle_refined_deg	1.48
r_nbd_other	0.229
r_nbd_refined	0.22
r_symmetry_vdw_other	0.2
r_nbtor_refined	0.19
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.146
r_metal_ion_refined	0.12
r_nbtor_other	0.112
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.085
r_bond_refined_d	0.018
r_gen_planes_other	0.011
r_gen_planes_refined	0.008
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1587
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
PHASER	phasing