6QU3 | pdb_00006qu3

Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb360

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		291	0.1M carboxylic acids (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate), buffer (0.1 M imidazole; MES monohydrate (acid)) and precipitant mix (40% v/v glycerol; 20% w/v PEG 4000).

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.154	α = 90
b = 150.561	β = 90
c = 83.993	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 S 6M		2015-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.35	69.07	99.89	10.8	9.5		88344

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	2.35	2.434

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	3f5m	2.35	68.66	83957	4390	99.91	0.20795	0.20597	0.21	0.24589	0.25	RANDOM	68.112

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]
1.35			1.73		-3.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.645
r_dihedral_angle_4_deg	15.852
r_dihedral_angle_3_deg	15.18
r_long_range_B_other	10.256
r_long_range_B_refined	10.254
r_dihedral_angle_1_deg	6.423
r_scangle_other	6.211
r_mcangle_it	5.539
r_mcangle_other	5.539
r_scbond_it	3.938
r_scbond_other	3.938
r_mcbond_it	3.743
r_mcbond_other	3.741
r_angle_refined_deg	1.333
r_angle_other_deg	1.196
r_chiral_restr	0.057
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
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	14025
Nucleic Acid Atoms
Solvent Atoms	402
Heterogen Atoms	163

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing