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Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to PTS1 peptide (10-SKL)
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 298K
Crystal Properties Matthews coefficient Solvent content 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.1 α = 90 b = 66.277 β = 104.7 c = 51.621 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 2006-08-28 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 32.95 96.3 0.06 11.1 2.71 19960 19221 3 29.14
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 79.1 0.311 2.5 1.82 1982
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 32.95 19217 981 96.29 0.214 0.212 0.219 0.257 0.2141 RANDOM 34.05
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] 0.03 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.247 r_dihedral_angle_4_deg 18.468 r_dihedral_angle_3_deg 15.904 r_dihedral_angle_1_deg 5.107 r_scangle_it 2.864 r_scbond_it 1.749 r_angle_refined_deg 1.095 r_mcangle_it 1.053 r_mcbond_it 0.604 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.247 r_dihedral_angle_4_deg 18.468 r_dihedral_angle_3_deg 15.904 r_dihedral_angle_1_deg 5.107 r_scangle_it 2.864 r_scbond_it 1.749 r_angle_refined_deg 1.095 r_mcangle_it 1.053 r_mcbond_it 0.604 r_nbtor_refined 0.302 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2182 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction d*TREK data scaling MOLREP phasing