2F4Z

Toxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E2 domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BEP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.429732% Peg 1500, 0.2 M MgCl2, 0.1 M Tris pH 8.4, 10 mM Spermidine, VAPOR DIFFUSION, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.3647.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.475α = 90
b = 141.334β = 90
c = 77.13γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVeriMax2005-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.125098.80.0770.0777.66.3233862338636.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.1697.30.7290.7292.226.31143

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2BEP2.1150226052260576398.660.199920.199920.19870.23779RANDOM35.401
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]
1.22-0.73-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.176
r_dihedral_angle_4_deg27.115
r_dihedral_angle_3_deg16.543
r_dihedral_angle_1_deg6.386
r_scangle_it4.977
r_scbond_it3.206
r_mcangle_it2.137
r_angle_refined_deg1.892
r_mcbond_it1.339
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.176
r_dihedral_angle_4_deg27.115
r_dihedral_angle_3_deg16.543
r_dihedral_angle_1_deg6.386
r_scangle_it4.977
r_scbond_it3.206
r_mcangle_it2.137
r_angle_refined_deg1.892
r_mcbond_it1.339
r_nbtor_refined0.315
r_symmetry_hbond_refined0.271
r_xyhbond_nbd_refined0.255
r_nbd_refined0.221
r_symmetry_vdw_refined0.15
r_chiral_restr0.129
r_bond_refined_d0.02
r_gen_planes_refined0.009
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 AtomsNumber
Protein Atoms2259
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building