4I70

Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KICIAGNH-363

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.82920.2M ammonium acetate, 18% PEG3350, pH 4.8, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.0138.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.04α = 90
b = 48.04β = 90
c = 216.11γ = 120
Symmetry
Space GroupP 32 1 2

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
11.672.03799.70.09922.529.83823538235-325.479
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)
11.61.799.30.3890.4185.947.56215

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 REPLACEMENTTHROUGHOUTIAGNH-3631.6723823238232191699.750.14380.14190.1817RANDOM19.1117
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]
-0.04-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.137
r_dihedral_angle_4_deg15.319
r_dihedral_angle_3_deg12.082
r_sphericity_free7.293
r_dihedral_angle_1_deg5.457
r_scangle_it4.619
r_scbond_it3.03
r_sphericity_bonded2.947
r_mcangle_it2.052
r_angle_refined_deg1.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.137
r_dihedral_angle_4_deg15.319
r_dihedral_angle_3_deg12.082
r_sphericity_free7.293
r_dihedral_angle_1_deg5.457
r_scangle_it4.619
r_scbond_it3.03
r_sphericity_bonded2.947
r_mcangle_it2.052
r_angle_refined_deg1.541
r_rigid_bond_restr1.429
r_mcbond_it1.305
r_angle_other_deg0.996
r_mcbond_other0.542
r_chiral_restr0.111
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2420
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms1

Software

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