2P0E

Human nicotinamide riboside kinase 1 in complex with tiazofurin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		same protein in complex with nicotinamide mononucleotide based on an isomorphous crystal

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9	291	20% PEG 3350, 0.2M Sodium phosphate monobasic, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.608	α = 90
b = 141.571	β = 90
c = 62.005	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		2007-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ DW	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	1.8	20	98.9	0.089	11	7.5		43446

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)
	1.8	1.86			0.526		7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	same protein in complex with nicotinamide mononucleotide based on an isomorphous crystal	1.8	19.838	22855	1181	98.897	0.176	0.1745	0.2092	14.171

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]
0.289			0.124		-0.413

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.513
r_dihedral_angle_4_deg	16.152
r_dihedral_angle_3_deg	12.111
r_dihedral_angle_1_deg	5.477
r_scangle_it	3.571
r_mcangle_it	3.109
r_scbond_it	2.526
r_mcbond_it	2.441
r_angle_refined_deg	1.45
r_angle_other_deg	0.934
r_mcbond_other	0.685
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.209
r_nbd_other	0.186
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.164
r_symmetry_vdw_other	0.159
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.09
r_nbtor_other	0.084
r_metal_ion_refined	0.071
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1581
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	24

Software

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