6QU3

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F5M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1M 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 coefficientSolvent content
2.3547.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.154α = 90
b = 150.561β = 90
c = 83.993γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3569.0799.8910.89.588344
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.434

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3f5m2.3568.6683957439099.910.207950.205970.24589RANDOM68.112
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]
1.351.73-3.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.645
r_dihedral_angle_4_deg15.852
r_dihedral_angle_3_deg15.18
r_long_range_B_other10.256
r_long_range_B_refined10.254
r_dihedral_angle_1_deg6.423
r_scangle_other6.211
r_mcangle_it5.539
r_mcangle_other5.539
r_scbond_it3.938
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.645
r_dihedral_angle_4_deg15.852
r_dihedral_angle_3_deg15.18
r_long_range_B_other10.256
r_long_range_B_refined10.254
r_dihedral_angle_1_deg6.423
r_scangle_other6.211
r_mcangle_it5.539
r_mcangle_other5.539
r_scbond_it3.938
r_scbond_other3.938
r_mcbond_it3.743
r_mcbond_other3.741
r_angle_refined_deg1.333
r_angle_other_deg1.196
r_chiral_restr0.057
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms14025
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms163

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing