9FSV

Yeast 20S proteasome with human beta2i (1-53) in complex with epoxyketone inhibitor 42


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CZ4Yeast 20S proteasome at 2.3 A resolution

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
3.6966.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.7α = 90
b = 300.6β = 112.83
c = 144.48γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-11-27MSINGLE 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
12.753094.90.0947.53259664
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)
12.752.850.64122.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.75302465291297694.930.21480.213110.24702RANDOM65.405
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]
2.5-1.57-1.40.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.495
r_dihedral_angle_4_deg16.669
r_dihedral_angle_3_deg16.387
r_dihedral_angle_1_deg7.419
r_long_range_B_refined4.007
r_long_range_B_other3.998
r_mcangle_it1.942
r_mcangle_other1.942
r_scangle_other1.616
r_angle_refined_deg1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.495
r_dihedral_angle_4_deg16.669
r_dihedral_angle_3_deg16.387
r_dihedral_angle_1_deg7.419
r_long_range_B_refined4.007
r_long_range_B_other3.998
r_mcangle_it1.942
r_mcangle_other1.942
r_scangle_other1.616
r_angle_refined_deg1.41
r_angle_other_deg1.228
r_mcbond_it1.084
r_mcbond_other1.084
r_scbond_it0.894
r_scbond_other0.891
r_chiral_restr0.055
r_bond_refined_d0.005
r_gen_planes_refined0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49516
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing