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Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb360
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 0.2128 0.24589 0.2519 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
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