6FDX

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1086

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	20% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.102	α = 90
b = 116.385	β = 108.67
c = 68.31	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	PIXEL	DECTRIS PILATUS3 6M	CRL	2016-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.31	57.1	97.1	0.051	0.061	0.033	0.999	12.3	3.4		36029

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.31	2.34	96.7		0.501	0.592	0.312	0.91	2.5	3.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.31	57.1	34309	1717	97.08	0.17218	0.16909	0.23191	RANDOM	66.101

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]
4.58		-0.71	1.73		-4.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.826
r_dihedral_angle_4_deg	18.035
r_dihedral_angle_3_deg	17.343
r_long_range_B_refined	10.491
r_long_range_B_other	10.485
r_scangle_other	7.923
r_mcangle_it	7.381
r_mcangle_other	7.38
r_dihedral_angle_1_deg	6.17
r_scbond_it	5.338
r_scbond_other	5.336
r_mcbond_it	5.053
r_mcbond_other	5.052
r_angle_refined_deg	1.607
r_angle_other_deg	1.032
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
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	5260
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	114

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
AutoPROC	data scaling
REFMAC	phasing