4I71

Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with a trypanocidal compound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KIC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION82920.1M Tris, 19% PEGMME2000, 10mM Ni2SO4, pH 8.0, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2144.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.36α = 90
b = 72.35β = 90
c = 133.28γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.28133.395.80.04816.643.47846778467-317.811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.281.3257.80.2640.3532.841.63472

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1KIC1.28133.37846778467394495.80.12690.12590.1467RANDOM14.8256
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]
0.04-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.482
r_dihedral_angle_3_deg12.971
r_sphericity_free11.817
r_dihedral_angle_4_deg10.523
r_dihedral_angle_1_deg6.177
r_scangle_it5.497
r_sphericity_bonded4.949
r_scbond_it4.023
r_mcangle_it3.106
r_mcbond_it2.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.482
r_dihedral_angle_3_deg12.971
r_sphericity_free11.817
r_dihedral_angle_4_deg10.523
r_dihedral_angle_1_deg6.177
r_scangle_it5.497
r_sphericity_bonded4.949
r_scbond_it4.023
r_mcangle_it3.106
r_mcbond_it2.308
r_rigid_bond_restr1.99
r_angle_refined_deg1.744
r_mcbond_other1.486
r_angle_other_deg1.037
r_chiral_restr0.121
r_bond_refined_d0.019
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 Atoms2496
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms33

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction