6QU4

Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb405

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F5M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		290	0.1M carboxylic acids (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium 154 potassium tartrate tetrahydrate and sodium oxamate), buffer system 1 (0.1 M imidazole; MES 155 monohydrate (acid)) and precipitant mix 3 (40% v/v glycerol; 20% w/v PEG 4000)

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.584	α = 90
b = 165.088	β = 90
c = 83.384	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS3 6M		2016-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9685	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.75	48.02	92.98	9.5	4		50992

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.848

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	3f5m	2.75	48.02	48489	2503	93.01	0.22029	0.21843	0.25694	RANDOM	62.15

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]
3.05			-8.69		5.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.17
r_dihedral_angle_4_deg	19.369
r_dihedral_angle_3_deg	16.943
r_dihedral_angle_1_deg	7.001
r_long_range_B_refined	5.975
r_long_range_B_other	5.975
r_scangle_other	2.801
r_mcangle_it	2.242
r_mcangle_other	2.242
r_scbond_it	1.793
r_scbond_other	1.793
r_angle_refined_deg	1.422
r_mcbond_it	1.327
r_mcbond_other	1.327
r_angle_other_deg	1.199
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
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	13845
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	172

Software

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