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Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Phosphofructokinase (PFK) PTS1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FCH PDB code 1FCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 298 2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.89 34.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.39 α = 90 b = 66.36 β = 105.13 c = 49.68 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 Osmic VariMax optics 2006-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.08 26.4 97.6 0.096 6.5 3.27 16165 16165 25.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.08 2.15 85.4 0.317 2.1 2.73
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 PDB code 1FCH 2.15 26.17 14844 753 97.36 0.215 0.212 0.2213 0.278 0.2273 RANDOM 23.242
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] -0.02 -0.01 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.186 r_dihedral_angle_3_deg 15.802 r_dihedral_angle_4_deg 14.135 r_dihedral_angle_1_deg 6.712 r_scangle_it 2.502 r_scbond_it 1.725 r_angle_refined_deg 1.368 r_mcangle_it 1.078 r_angle_other_deg 1.008 r_mcbond_it 0.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.186 r_dihedral_angle_3_deg 15.802 r_dihedral_angle_4_deg 14.135 r_dihedral_angle_1_deg 6.712 r_scangle_it 2.502 r_scbond_it 1.725 r_angle_refined_deg 1.368 r_mcangle_it 1.078 r_angle_other_deg 1.008 r_mcbond_it 0.904 r_symmetry_vdw_other 0.238 r_nbd_refined 0.222 r_nbd_other 0.195 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.155 r_mcbond_other 0.151 r_symmetry_vdw_refined 0.147 r_nbtor_other 0.11 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2332 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Crystal data collection d*TREK data reduction d*TREK data scaling MOLREP phasing