3CVN

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FCHPDB code 1FCH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2982.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8 - 5.0, vapor diffusion, sitting drop, temperature 298KK
Crystal Properties
Matthews coefficientSolvent content
1.9938.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.619α = 90
b = 66.178β = 104.55
c = 51.979γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944Osmic VariMax optics2006-12-07SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1243.1997.60.0988.43.481992519415524.79
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0781.30.3162.22.321538

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB code 1FCH240.061941198397.590.1960.1920.265RANDOM25.734
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.446
r_dihedral_angle_4_deg15.75
r_dihedral_angle_3_deg14.717
r_dihedral_angle_1_deg5.225
r_scangle_it2.916
r_scbond_it2
r_angle_refined_deg1.333
r_mcangle_it1.095
r_angle_other_deg0.976
r_mcbond_it0.945
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.446
r_dihedral_angle_4_deg15.75
r_dihedral_angle_3_deg14.717
r_dihedral_angle_1_deg5.225
r_scangle_it2.916
r_scbond_it2
r_angle_refined_deg1.333
r_mcangle_it1.095
r_angle_other_deg0.976
r_mcbond_it0.945
r_symmetry_vdw_other0.256
r_nbd_refined0.221
r_nbd_other0.196
r_nbtor_refined0.178
r_symmetry_vdw_refined0.171
r_mcbond_other0.169
r_xyhbond_nbd_refined0.154
r_symmetry_hbond_refined0.141
r_nbtor_other0.088
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2375
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms88

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata reduction
MOLREPphasing