5F6Y

Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U9B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52940.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000
Crystal Properties
Matthews coefficientSolvent content
2.7154.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.237α = 90
b = 35.492β = 111.82
c = 58.122γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDMARMOSAIC 300 mm CCD2013-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
11.145094.40.04630.83.465740
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)
11.141.1667.50.26932.6

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 REPLACEMENTTHROUGHOUT1U9B1.145062405331194.390.15670.155590.17777RANDOM10.817
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]
-0.4-0.64-0.410.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.315
r_dihedral_angle_4_deg17.231
r_dihedral_angle_3_deg10.301
r_scangle_it5.805
r_dihedral_angle_1_deg5.69
r_scbond_it3.885
r_mcangle_it2.88
r_angle_refined_deg1.941
r_mcbond_it1.865
r_rigid_bond_restr1.569
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.315
r_dihedral_angle_4_deg17.231
r_dihedral_angle_3_deg10.301
r_scangle_it5.805
r_dihedral_angle_1_deg5.69
r_scbond_it3.885
r_mcangle_it2.88
r_angle_refined_deg1.941
r_mcbond_it1.865
r_rigid_bond_restr1.569
r_angle_other_deg0.946
r_mcbond_other0.536
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1241
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing