2BF8

Crystal structure of SUMO modified ubiquitin conjugating enzyme E2- 25K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FZYPDB ENTRY 1FZY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5100 MM TRIS PH 8.5 200 MM MAGNESIUM CHLORIDE 17% PEG 4000 10 % GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.448.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.391α = 90
b = 58.391β = 90
c = 162.842γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100ADSC ADSC Q4RTOROIDAL MIRROR2003-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.35099.90.0730.613.413257-3
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)
12.32.4299.50.533.813

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FZY2.355.051254565199.60.2130.210.279RANDOM53.66
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]
-2.04-2.044.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.697
r_dihedral_angle_4_deg20.63
r_dihedral_angle_3_deg17.644
r_dihedral_angle_1_deg7.276
r_scangle_it2.496
r_scbond_it1.755
r_angle_refined_deg1.64
r_mcangle_it0.979
r_angle_other_deg0.927
r_mcbond_it0.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.697
r_dihedral_angle_4_deg20.63
r_dihedral_angle_3_deg17.644
r_dihedral_angle_1_deg7.276
r_scangle_it2.496
r_scbond_it1.755
r_angle_refined_deg1.64
r_mcangle_it0.979
r_angle_other_deg0.927
r_mcbond_it0.813
r_symmetry_hbond_refined0.319
r_symmetry_vdw_other0.272
r_nbd_refined0.198
r_nbd_other0.19
r_nbtor_refined0.183
r_mcbond_other0.173
r_xyhbond_nbd_refined0.165
r_chiral_restr0.095
r_nbtor_other0.089
r_symmetry_vdw_refined0.075
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1853
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing