2A4D

Structure of the human ubiquitin-conjugating enzyme E2 variant 1 (UEV-1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J7DPDB ENTRY 1J7D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529832% PEG1500, 0.2 M NaCl, 1 mM DTT, 0.1 M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
1.9135.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.058α = 90
b = 53.91β = 90
c = 108.034γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MIRRORS2005-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
11.693096.40.038445.913994-3
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)
11.691.7596.40.3322.72.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1J7D1.6930139661326270496.80.1850.1830.24RANDOM31.28
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]
-0.710.230.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.068
r_dihedral_angle_4_deg17.991
r_dihedral_angle_3_deg14.956
r_sphericity_free6.923
r_scangle_it6.073
r_dihedral_angle_1_deg5.47
r_scbond_it5.101
r_sphericity_bonded4.924
r_mcangle_it3.806
r_rigid_bond_restr3.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.068
r_dihedral_angle_4_deg17.991
r_dihedral_angle_3_deg14.956
r_sphericity_free6.923
r_scangle_it6.073
r_dihedral_angle_1_deg5.47
r_scbond_it5.101
r_sphericity_bonded4.924
r_mcangle_it3.806
r_rigid_bond_restr3.74
r_mcbond_it2.869
r_angle_refined_deg1.552
r_nbtor_refined0.318
r_symmetry_vdw_refined0.248
r_nbd_refined0.225
r_symmetry_hbond_refined0.211
r_xyhbond_nbd_refined0.151
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.007
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1104
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing