5GO1

Structural, Functional characterization and discovery of novel inhibitors of Leishmania amazonensis Nucleoside Diphosphatase Kinase (NDK)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NGR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG MME 500, Bis-Tris Propane, Magnesium chloride, 30% ethylene glycol used as cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.18	α = 90
b = 115.18	β = 90
c = 62.18	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	MARMOSAIC 225 mm CCD	bent collimating mirror and toroid	2012-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.954	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	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	99.75	98.4	0.072	0.075	0.99	19.8	13.8		8621			65.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	95.2		0.79	0.768	2.3	10.1

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	3NGR	2.5	99.75	8201	407	97.29	0.22707	0.22525	0.2655	RANDOM	72.575

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]
1.44	0.72		1.44		-4.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.973
r_dihedral_angle_3_deg	20.167
r_dihedral_angle_4_deg	18.905
r_long_range_B_other	16.561
r_long_range_B_refined	16.554
r_mcangle_it	12.17
r_mcangle_other	12.159
r_scangle_other	10.762
r_mcbond_it	8.423
r_mcbond_other	8.411
r_dihedral_angle_1_deg	7.423
r_scbond_it	7.062
r_scbond_other	7.062
r_angle_refined_deg	1.992
r_angle_other_deg	1.172
r_chiral_restr	0.124
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002
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	814
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing