2QSZ

Human nicotinamide riboside kinase 1 in complex with nicotinamide mononucleotide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	20% PEG 3350, 0.2M Sodium phosphate monobasic, 0.15M D(+)sucrose, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.921	α = 90
b = 142.342	β = 90
c = 62.434	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	IMAGE PLATE	RIGAKU RAXIS		2007-01-26	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	1.9	30	99.1	0.138	6.4	4.8		19738

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	98.1		0.901		4.2	1906

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 2QSY	1.9	23.64	19721	1031	98.63	0.219	0.217	0.255	Reflections from isomorphous data of NRK1-ADP complex	21.061

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]
0.03			0.28		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.625
r_dihedral_angle_4_deg	18.199
r_dihedral_angle_3_deg	13.255
r_dihedral_angle_1_deg	5.757
r_angle_other_deg	4.119
r_scangle_it	2.905
r_mcangle_it	2.84
r_scbond_it	2.156
r_mcbond_it	2.069
r_angle_refined_deg	1.323
r_nbd_other	0.228
r_nbd_refined	0.196
r_nbtor_refined	0.177
r_symmetry_vdw_other	0.168
r_symmetry_vdw_refined	0.156
r_xyhbond_nbd_refined	0.123
r_symmetry_hbond_refined	0.117
r_nbtor_other	0.108
r_chiral_restr	0.079
r_bond_refined_d	0.015
r_gen_planes_other	0.007
r_gen_planes_refined	0.005
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1559
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	35

Software

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