3MHS

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.6α = 90
b = 102.084β = 90
c = 120.903γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors with two additional horizontally deflecting mirrors2010-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.94944APS23-ID-B

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
11.8935.199.80.0960.09629.513.7780117392822
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)
1.891.9398.80.8860.8862.258.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.8935.173928393499.260.161480.159040.20757RANDOM30.086
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]
0.480.18-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg16.456
r_dihedral_angle_3_deg14.993
r_dihedral_angle_1_deg5.499
r_scangle_it5.245
r_scbond_it3.792
r_mcangle_it2.293
r_angle_refined_deg1.399
r_mcbond_it1.347
r_angle_other_deg0.859
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg16.456
r_dihedral_angle_3_deg14.993
r_dihedral_angle_1_deg5.499
r_scangle_it5.245
r_scbond_it3.792
r_mcangle_it2.293
r_angle_refined_deg1.399
r_mcbond_it1.347
r_angle_other_deg0.859
r_mcbond_other0.428
r_chiral_restr0.18
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6391
Nucleic Acid Atoms
Solvent Atoms845
Heterogen Atoms18

Software

Software
Software NamePurpose
Blu-Icedata collection
SHELXDphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling