2AYV

Crystal structure of a putative ubiquitin-conjugating enzyme E2 from Toxoplasma gondii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X23 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62913.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.753.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.553α = 90
b = 85.611β = 90
c = 89.612γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2005-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
122099.20.0385.712360
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1596.20.3315.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1X232.001201235959799.3330.2280.22610.258RANDOM20.822
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]
1.9840.39-2.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.319
r_dihedral_angle_3_deg14.402
r_dihedral_angle_4_deg8.024
r_dihedral_angle_1_deg6.15
r_scangle_it3.666
r_mcangle_it3.303
r_scbond_it2.869
r_mcbond_it2.453
r_angle_refined_deg1.408
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.319
r_dihedral_angle_3_deg14.402
r_dihedral_angle_4_deg8.024
r_dihedral_angle_1_deg6.15
r_scangle_it3.666
r_mcangle_it3.303
r_scbond_it2.869
r_mcbond_it2.453
r_angle_refined_deg1.408
r_nbtor_refined0.305
r_symmetry_vdw_refined0.296
r_symmetry_hbond_refined0.212
r_nbd_refined0.181
r_xyhbond_nbd_refined0.141
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1132
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms10

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction