1YF9

Structural analysis of Leishmania major ubiquitin conjugating enzyme E2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72983 M Sodium chloride 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.0469.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.448α = 90
b = 114.448β = 90
c = 139.547γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-12-09MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.97957, 0.95372, 0.97975ALS8.2.1

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
125091.670.07713.36.3549155491537.14
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)
122.10861.170.8181.645243

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2505491554915291991.670.186130.186130.184860.21039RANDOM47.006
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]
-0.45-0.450.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.495
r_dihedral_angle_4_deg15.649
r_dihedral_angle_3_deg14.488
r_dihedral_angle_1_deg5.428
r_scangle_it3.937
r_scbond_it3.001
r_mcangle_it1.931
r_mcbond_it1.212
r_angle_refined_deg1.153
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.495
r_dihedral_angle_4_deg15.649
r_dihedral_angle_3_deg14.488
r_dihedral_angle_1_deg5.428
r_scangle_it3.937
r_scbond_it3.001
r_mcangle_it1.931
r_mcbond_it1.212
r_angle_refined_deg1.153
r_nbtor_refined0.303
r_symmetry_vdw_refined0.21
r_nbd_refined0.187
r_symmetry_hbond_refined0.187
r_xyhbond_nbd_refined0.128
r_chiral_restr0.088
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms3882
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SHELXSphasing