5L5J

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 14


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 = 135.69α = 90
b = 299.81β = 112.76
c = 145.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-07-11MSINGLE 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
12.93097.20.07313.83.1229789
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)
12.9398.90.5612.7

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 REPLACEMENTTHROUGHOUT5CZ42.9152182991149097.270.173390.1720.20001RANDOM66.534
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]
1.88-0.43-5.022.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.925
r_sphericity_free29.913
r_sphericity_bonded14.976
r_dihedral_angle_3_deg14.473
r_dihedral_angle_4_deg14.228
r_dihedral_angle_1_deg4.821
r_long_range_B_refined3.924
r_long_range_B_other3.923
r_mcangle_it3.426
r_mcangle_other3.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.925
r_sphericity_free29.913
r_sphericity_bonded14.976
r_dihedral_angle_3_deg14.473
r_dihedral_angle_4_deg14.228
r_dihedral_angle_1_deg4.821
r_long_range_B_refined3.924
r_long_range_B_other3.923
r_mcangle_it3.426
r_mcangle_other3.426
r_scangle_other3.204
r_scbond_it2.622
r_scbond_other2.622
r_mcbond_it2.556
r_mcbond_other2.556
r_rigid_bond_restr1.018
r_angle_refined_deg0.984
r_angle_other_deg0.843
r_chiral_restr0.051
r_bond_refined_d0.005
r_gen_planes_refined0.003
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 Atoms49382
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms214

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement