2QT0

Human nicotinamide riboside kinase 1 in complex with nicotinamide riboside and an ATP analogue

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	8	291	35% PEG 2000 MME, 0.1M Tris-HCl. The protein solution (40mg/mL) contained 0.01M Nicotinamide riboside, 0.01M AMPPNP and 0.02M Magnesium chloride, pH 8.0, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.025	α = 90
b = 97.025	β = 90
c = 44.801	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS		2007-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.92	30	100	0.086	10.7	6.5		31229

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)
	1.92	1.99	100		0.999		6.2	3112

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2P0E	1.92	30	16835	851	99.91	0.211	0.209	0.241	RANDOM	27.811

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]
0.3			0.3		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.841
r_dihedral_angle_3_deg	13.375
r_dihedral_angle_4_deg	10.315
r_dihedral_angle_1_deg	5.811
r_angle_other_deg	4.146
r_mcangle_it	3.348
r_scangle_it	3.15
r_scbond_it	2.408
r_mcbond_it	2.349
r_angle_refined_deg	1.416
r_symmetry_vdw_refined	0.409
r_symmetry_vdw_other	0.323
r_nbd_other	0.235
r_nbd_refined	0.207
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.161
r_nbtor_other	0.123
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.083
r_bond_refined_d	0.017
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1457
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	50

Software

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