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Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to PTS1 peptide (7-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 4.8 298 2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8 - 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298KK, pH 4.80
Crystal Properties Matthews coefficient Solvent content 3.64 66.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.794 α = 90 b = 68.794 β = 90 c = 230.232 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315 2006-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 3 50 99.9 0.09 22.7 8 11776 96.04
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) 1 3 3.11 99.5 0.0704 2.6 8.5
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 3.01 47.62 11705 584 99.7 0.275 0.273 0.3168 0.321 0.3136 RANDOM 97.12
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 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.329 r_dihedral_angle_3_deg 20.441 r_dihedral_angle_4_deg 11.169 r_dihedral_angle_1_deg 7.46 r_scangle_it 1.488 r_angle_refined_deg 1.487 r_scbond_it 0.918 r_mcangle_it 0.639 r_mcbond_it 0.356 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.329 r_dihedral_angle_3_deg 20.441 r_dihedral_angle_4_deg 11.169 r_dihedral_angle_1_deg 7.46 r_scangle_it 1.488 r_angle_refined_deg 1.487 r_scbond_it 0.918 r_mcangle_it 0.639 r_mcbond_it 0.356 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.285 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.114 r_bond_refined_d 0.011 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2266 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing