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Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb12
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 9.5% PEG, 8000, 0.1 M sodium cacodylate pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.42 49.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.251 α = 90 b = 132.513 β = 90 c = 282.699 γ = 90
Symmetry Space Group P 21 21 21
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 2014-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 3.4 96.67 99.73 8.4 4.4 60210
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 3.4 3.522
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 3.4 96.67 57240 2969 99.77 0.25054 0.24968 0.2446 0.2671 0.2619 RANDOM 120.881
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] 5.37 5.64 -11.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.017 r_dihedral_angle_3_deg 19.304 r_dihedral_angle_4_deg 17.033 r_dihedral_angle_1_deg 6.996 r_angle_refined_deg 1.484 r_angle_other_deg 1.209 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.017 r_dihedral_angle_3_deg 19.304 r_dihedral_angle_4_deg 17.033 r_dihedral_angle_1_deg 6.996 r_angle_refined_deg 1.484 r_angle_other_deg 1.209 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28111 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing