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Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb405
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3f5m 2.75 48.02 48489 2503 93.01 0.22029 0.21843 0.2152 0.25694 0.2535 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
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