3R9L

Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NPK	PDB ENTRY 1NPK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	289	GilaA.00438.a.A1 PW27083 at 24.97 mg/mL in 25 mM Hepes pH 7.0, 0.5 M NaCl, 5% glycerol, 2 mM DTT, 0.025% azide against CSHT C11 focus screen 0.1 M Hepes pH 7.0, 0.9 M Na phosphate, 0.9 M K phosphate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 216300h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.62	65.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.96	α = 90
b = 116.96	β = 90
c = 62.69	γ = 120

Symmetry
Space Group	P 63 2 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	CCD	ADSC QUANTUM 315r		2011-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97946	ALS	5.0.1

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	2.65	50	98.8	0.049	26.02	5.6	7760	7665		-3	60.858

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)
	2.65	2.72	100		0.526	3.26	6	567

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1NPK	2.65	39.4	7619	348	98.26	0.2359	0.2344	0.2663	RANDOM	78.7938

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]
1.33	0.67		1.33		-2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.361
r_dihedral_angle_4_deg	28.396
r_dihedral_angle_3_deg	14.313
r_dihedral_angle_1_deg	6.811
r_scangle_it	2.695
r_mcangle_it	1.571
r_scbond_it	1.539
r_angle_refined_deg	1.278
r_mcbond_it	0.854
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.361
r_dihedral_angle_4_deg	28.396
r_dihedral_angle_3_deg	14.313
r_dihedral_angle_1_deg	6.811
r_scangle_it	2.695
r_mcangle_it	1.571
r_scbond_it	1.539
r_angle_refined_deg	1.278
r_mcbond_it	0.854
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	813
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.