6HVR

Yeast 20S proteasome with human beta2i (1-53) 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 = 135.77α = 90
b = 299.59β = 113.24
c = 144.64γ = 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
12.75098.70.0898.73.1286280
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)
12.72.899.70.5292.1

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 REPLACEMENTTHROUGHOUT5CZ42.7152703981423198.290.19260.191240.21868RANDOM68.037
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]
2.340.27-5.442.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.278
r_sphericity_free32.601
r_dihedral_angle_3_deg14.649
r_dihedral_angle_4_deg14.142
r_dihedral_angle_1_deg5.818
r_sphericity_bonded5.741
r_long_range_B_refined3.275
r_long_range_B_other3.231
r_mcangle_it2.753
r_mcangle_other2.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.278
r_sphericity_free32.601
r_dihedral_angle_3_deg14.649
r_dihedral_angle_4_deg14.142
r_dihedral_angle_1_deg5.818
r_sphericity_bonded5.741
r_long_range_B_refined3.275
r_long_range_B_other3.231
r_mcangle_it2.753
r_mcangle_other2.753
r_scangle_other2.438
r_mcbond_it2.047
r_mcbond_other2.047
r_scbond_it1.996
r_scbond_other1.995
r_rigid_bond_restr1.287
r_angle_refined_deg1.188
r_angle_other_deg0.908
r_chiral_restr0.068
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 Atoms49340
Nucleic Acid Atoms
Solvent Atoms636
Heterogen Atoms190

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement