5U7X

Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Vigna unguiculata subsp. cylindrica (Dolichos biflorus) in complex with phosphate and manganese

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291	0.2 M MgCl2, 50 mM acetate, pH 5.0, 9-12% MPD, 10-2-% PEG 3350, 5 mM AMP

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.09	α = 90
b = 71.11	β = 139.45
c = 93.27	γ = 90

Symmetry
Space Group	C 1 2 1

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		2011-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	2.6	46.62	100	0.099	15.9	7.5		15843			30.59

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	5u7p	2.6	46.62	15045	789	99.92	0.17191	0.16796	0.24804	RANDOM	31.664

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		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.939
r_dihedral_angle_3_deg	18.388
r_dihedral_angle_4_deg	18.289
r_dihedral_angle_1_deg	7.356
r_long_range_B_refined	5.724
r_long_range_B_other	5.668
r_scangle_other	4.018
r_mcangle_it	3.019
r_mcangle_other	3.018
r_scbond_it	2.528
r_scbond_other	2.525
r_mcbond_it	1.925
r_mcbond_other	1.923
r_angle_refined_deg	1.89
r_angle_other_deg	0.903
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3147
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing