5G5V

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-038

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I15	PDB ENTRY 4I15

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 PH 6.5; VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 4 DEGREES

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.69	α = 90
b = 114.781	β = 109.4
c = 64.009	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 PIXEL	CRL	2015-08-03	M	SINGLE WAVELENGTH

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

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	1.8	88.58	97.9	0.1	7.1	3.2		90889

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	1.8	1.83	97		0.6	2.1	3.2

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	PDB ENTRY 4I15	1.8	88.58	86430	4449	97.72	0.17748	0.17637	0.19872	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.539
r_dihedral_angle_3_deg	13.123
r_dihedral_angle_4_deg	12.081
r_long_range_B_refined	5.453
r_long_range_B_other	5.453
r_dihedral_angle_1_deg	5.04
r_scangle_other	2.767
r_mcangle_it	2.077
r_mcangle_other	2.077
r_scbond_it	1.683
r_scbond_other	1.683
r_angle_refined_deg	1.336
r_mcbond_it	1.222
r_mcbond_other	1.222
r_angle_other_deg	0.997
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
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	5280
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing