6HUB

Yeast 20S proteasome with human beta2c (S171G) in complex with 16


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 = 135.16α = 90
b = 299.38β = 113.09
c = 144.81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-11-20MSINGLE 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
12.95098.80.0988.23.1230576
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)
12.930.562

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 REPLACEMENTTHROUGHOUT5CZ42.9152174691144598.20.18580.184440.2118RANDOM65.601
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]
1.86-1.81-5.093.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.103
r_sphericity_free31.899
r_dihedral_angle_3_deg14.955
r_dihedral_angle_4_deg14.506
r_sphericity_bonded6.266
r_dihedral_angle_1_deg5.906
r_long_range_B_refined3.512
r_long_range_B_other3.483
r_mcangle_it2.953
r_mcangle_other2.952
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.103
r_sphericity_free31.899
r_dihedral_angle_3_deg14.955
r_dihedral_angle_4_deg14.506
r_sphericity_bonded6.266
r_dihedral_angle_1_deg5.906
r_long_range_B_refined3.512
r_long_range_B_other3.483
r_mcangle_it2.953
r_mcangle_other2.952
r_scangle_other2.617
r_mcbond_it2.267
r_mcbond_other2.267
r_scbond_it2.219
r_scbond_other2.218
r_angle_refined_deg1.197
r_rigid_bond_restr1.146
r_angle_other_deg0.925
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms48944
Nucleic Acid Atoms
Solvent Atoms591
Heterogen Atoms200

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement