6HVW

Yeast 20S proteasome with human beta2i (1-53) in complex with 43


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 = 134.24α = 90
b = 299.9β = 112.5
c = 143.25γ = 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
135098.20.09111.83.1204830
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)
133.199.20.5922.2

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 REPLACEMENTTHROUGHOUT5CZ43151930541016197.580.166480.164610.20199RANDOM75.079
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]
2.1-1.82-3.111.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_sphericity_free34.02
r_sphericity_bonded25.818
r_dihedral_angle_3_deg14.654
r_dihedral_angle_4_deg14.146
r_dihedral_angle_1_deg5.932
r_long_range_B_refined5.769
r_long_range_B_other5.76
r_mcangle_it5.098
r_mcangle_other5.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_sphericity_free34.02
r_sphericity_bonded25.818
r_dihedral_angle_3_deg14.654
r_dihedral_angle_4_deg14.146
r_dihedral_angle_1_deg5.932
r_long_range_B_refined5.769
r_long_range_B_other5.76
r_mcangle_it5.098
r_mcangle_other5.098
r_scangle_other4.427
r_mcbond_it3.674
r_mcbond_other3.674
r_scbond_it3.417
r_scbond_other3.417
r_rigid_bond_restr1.441
r_angle_refined_deg1.238
r_angle_other_deg0.988
r_chiral_restr0.101
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 Atoms198
Heterogen Atoms266

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing