6FDS | pdb_00006fds

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-226

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.72	α = 90
b = 120.17	β = 108.05
c = 68.17	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	2015-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	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	2.2	79.98	99.5	0.05	0.062	0.035	0.998	10.1	2.8		43570

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	2.2	2.32	99.7		0.364	0.447	0.256	0.902	2.5	2.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4I15	2.2	79.98	41186	2191	99.06	0.1954	0.19303	0.2	0.23959	0.25	RANDOM	62.717

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]
6.6		0.32	-1.78		-4.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.772
r_dihedral_angle_4_deg	19.392
r_dihedral_angle_3_deg	16.37
r_long_range_B_other	11.169
r_long_range_B_refined	11.162
r_scangle_other	8.297
r_mcangle_it	7.871
r_mcangle_other	7.87
r_scbond_it	5.554
r_scbond_other	5.553
r_dihedral_angle_1_deg	5.52
r_mcbond_it	5.431
r_mcbond_other	5.418
r_angle_refined_deg	1.612
r_angle_other_deg	1.042
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
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	178
Heterogen Atoms	114

Software

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