5L5T

Yeast 20S proteasome with human beta5i (1-138; V31M) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 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 = 135.75α = 90
b = 300.02β = 113.05
c = 145.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-12-10MSINGLE 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
12.93098.50.07914.84232923
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)
12.9399.30.5473.5

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 REPLACEMENTTHROUGHOUT5CZ42.9152212761164798.670.172390.171170.19533RANDOM64.918
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]
3.33-0.76-4.721.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.016
r_sphericity_free33.62
r_dihedral_angle_3_deg14.306
r_dihedral_angle_4_deg14.16
r_sphericity_bonded12.582
r_dihedral_angle_1_deg4.826
r_long_range_B_refined3.758
r_long_range_B_other3.75
r_mcangle_it3.264
r_mcangle_other3.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.016
r_sphericity_free33.62
r_dihedral_angle_3_deg14.306
r_dihedral_angle_4_deg14.16
r_sphericity_bonded12.582
r_dihedral_angle_1_deg4.826
r_long_range_B_refined3.758
r_long_range_B_other3.75
r_mcangle_it3.264
r_mcangle_other3.264
r_scangle_other3.089
r_scbond_it2.532
r_scbond_other2.532
r_mcbond_it2.449
r_mcbond_other2.449
r_rigid_bond_restr0.968
r_angle_refined_deg0.875
r_angle_other_deg0.707
r_chiral_restr0.049
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms49384
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing