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Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) 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 298 2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8 - 5.0, vapor diffusion, sitting drop, temperature 298KK
Crystal Properties Matthews coefficient Solvent content 1.99 38.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.619 α = 90 b = 66.178 β = 104.55 c = 51.979 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 2006-12-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 43.19 97.6 0.098 8.4 3.48 19925 19415 5 24.79
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 2.07 81.3 0.316 2.2 2.32 1538
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 40.06 19411 983 97.59 0.196 0.192 0.2053 0.265 0.1954 RANDOM 25.734
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.446 r_dihedral_angle_4_deg 15.75 r_dihedral_angle_3_deg 14.717 r_dihedral_angle_1_deg 5.225 r_scangle_it 2.916 r_scbond_it 2 r_angle_refined_deg 1.333 r_mcangle_it 1.095 r_angle_other_deg 0.976 r_mcbond_it 0.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.446 r_dihedral_angle_4_deg 15.75 r_dihedral_angle_3_deg 14.717 r_dihedral_angle_1_deg 5.225 r_scangle_it 2.916 r_scbond_it 2 r_angle_refined_deg 1.333 r_mcangle_it 1.095 r_angle_other_deg 0.976 r_mcbond_it 0.945 r_symmetry_vdw_other 0.256 r_nbd_refined 0.221 r_nbd_other 0.196 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.171 r_mcbond_other 0.169 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.088 r_chiral_restr 0.086 r_bond_refined_d 0.013 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 2375 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 88
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection d*TREK data reduction MOLREP phasing