6HV4

Yeast 20S proteasome with human beta2i (1-53) in complex with ONX 0914


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CZ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.99α = 90
b = 298.78β = 112.52
c = 143.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
135097.20.093103.2203267
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)
133.1990.5733.2

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 REPLACEMENTTHROUGHOUT5CZ43151915841008496.570.18530.183790.21382RANDOM74.111
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]
3.19-2.84-5.683.61
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.004
r_dihedral_angle_2_deg35.294
r_dihedral_angle_4_deg14.896
r_dihedral_angle_3_deg14.686
r_sphericity_bonded7.636
r_dihedral_angle_1_deg5.901
r_long_range_B_refined4.447
r_long_range_B_other4.424
r_mcangle_it3.845
r_mcangle_other3.845
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.004
r_dihedral_angle_2_deg35.294
r_dihedral_angle_4_deg14.896
r_dihedral_angle_3_deg14.686
r_sphericity_bonded7.636
r_dihedral_angle_1_deg5.901
r_long_range_B_refined4.447
r_long_range_B_other4.424
r_mcangle_it3.845
r_mcangle_other3.845
r_scangle_other3.298
r_mcbond_it2.796
r_mcbond_other2.796
r_scbond_it2.635
r_scbond_other2.635
r_angle_refined_deg1.225
r_rigid_bond_restr1.172
r_angle_other_deg0.947
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.003
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49164
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms320

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement