5L8Y

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-937

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
2.85	56.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.82	α = 90
b = 115.94	β = 107.43
c = 68.51	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 PILATUS 6M-F	CRL	2013-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.14	57.97	97.7	0.057	0.998	13.4	3.3		45186

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	2.14	2.2	98.1		0.578	2.2	3.1

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	2.14	57.97	43013	2162	97.56	0.18259	0.18085	0.21684	RANDOM	51.13

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]
4.24		-0.85	1.77		-4.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.036
r_dihedral_angle_3_deg	15.322
r_dihedral_angle_4_deg	14.292
r_long_range_B_refined	8.423
r_long_range_B_other	8.423
r_scangle_other	6.212
r_dihedral_angle_1_deg	5.432
r_mcangle_it	5.238
r_mcangle_other	5.238
r_scbond_it	4.065
r_scbond_other	4.064
r_mcbond_it	3.46
r_mcbond_other	3.458
r_angle_refined_deg	1.461
r_angle_other_deg	1.191
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005
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	308
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Coot	model building