3JS9

Crystal structure of nucleoside diphosphate kinase family protein from Babesia bovis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VU5	trimer generate from 2VU5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	CSHT condition A4, 2.0 M ammonium sulfate, 0.1 M Tris pH 8.5; 0.4:0.4 uL drops; 31.2 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% glycerol, 2 mM DTT; crystal tracking ID 204382a4; non-cleavable expression tag, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.894	α = 90
b = 125.894	β = 90
c = 101.512	γ = 90

Symmetry
Space Group	P 43 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	CCD	ADSC QUANTUM 315		2009-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976484	ALS	5.0.3

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	2.5	50	99.5	0.149	14.3	9.2		28787

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	2.5	2.59	97.2		0.677	2.4	7.6	2742

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	trimer generate from 2VU5	2.5	47.08	28727	1464	99.27	0.179	0.176	0.221	RANDOM	28.414

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]
-2.3			-2.3		4.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.58
r_dihedral_angle_4_deg	22.979
r_dihedral_angle_3_deg	15.537
r_dihedral_angle_1_deg	5.978
r_scangle_it	3.301
r_scbond_it	2.093
r_angle_refined_deg	1.466
r_mcangle_it	1.253
r_mcbond_it	0.65
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3478
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	65

Software

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