2QSY | pdb_00002qsy

Human nicotinamide riboside kinase 1 in complex with ADP

X-RAY DIFFRACTION

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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
2.47	50.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.453	α = 90
b = 142.07	β = 90
c = 62.263	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	ADSC QUANTUM 4		2006-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.97931	APS	17-ID

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	50	99.6	0.122	6.4	6.9		19430

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	96.6		0.709		5.4	1857

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.95	28.51	17990	933	99.78	0.222	0.222	0.219	0.2243	0.263	0.2635	RANDOM	18.786

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]
0.25			-0.04		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.986
r_dihedral_angle_4_deg	17.76
r_dihedral_angle_3_deg	13.731
r_dihedral_angle_1_deg	5.479
r_angle_other_deg	4.148
r_mcangle_it	3.562
r_scangle_it	3.409
r_scbond_it	2.604
r_mcbond_it	2.531
r_angle_refined_deg	1.46
r_nbd_other	0.229
r_symmetry_vdw_other	0.21
r_nbd_refined	0.203
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_refined	0.149
r_nbtor_other	0.108
r_chiral_restr	0.082
r_bond_refined_d	0.016
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d
r_metal_ion_refined
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1480
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	33

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction