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Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Phosphoglucoisomerase (PGI) PTS1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model ModelArchive MA-CPS7U ENTRY 1FHC that was moved from PDB to ModelArchive
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 2.04 39.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.405 α = 90 b = 66.404 β = 104.47 c = 52.117 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 2006-12-07 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 43.96 97.7 0.105 7.2 3.49 19875 19875 25.2
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 81.1 0.38 1.9 2.33 2015
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 ENTRY 1FHC 2 40.19 19869 1013 97.71 0.192 0.189 0.2009 0.234 0.2029 RANDOM 27.13
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.636 r_dihedral_angle_4_deg 15.533 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_1_deg 5.734 r_scangle_it 2.942 r_scbond_it 2.052 r_angle_refined_deg 1.327 r_mcangle_it 1.155 r_mcbond_it 1.01 r_angle_other_deg 0.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.636 r_dihedral_angle_4_deg 15.533 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_1_deg 5.734 r_scangle_it 2.942 r_scbond_it 2.052 r_angle_refined_deg 1.327 r_mcangle_it 1.155 r_mcbond_it 1.01 r_angle_other_deg 0.989 r_symmetry_vdw_refined 0.263 r_symmetry_vdw_other 0.261 r_nbd_refined 0.22 r_nbd_other 0.185 r_mcbond_other 0.184 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.156 r_nbtor_other 0.087 r_chiral_restr 0.081 r_bond_other_d 0.016 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2415 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 48
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction MOLREP phasing