6H39

Yeast 20S proteasome in complex with the peptidic non-covalent binding inhibitor RTS-V5


X-RAY DIFFRACTION

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 = 137.14α = 90
b = 300.78β = 113.48
c = 145.08γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-07-15MSINGLE 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
12.55097.90.05114.73.2362822
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)
12.52.698.60.5682.5

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 REPLACEMENTTHROUGHOUT5CZ42.5153431371805997.590.188660.187170.21693RANDOM69.413
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]
1.08-0.69-1.891.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.539
r_dihedral_angle_2_deg34.512
r_sphericity_bonded24.977
r_dihedral_angle_4_deg14.788
r_dihedral_angle_3_deg14.34
r_dihedral_angle_1_deg5.587
r_long_range_B_refined4.946
r_long_range_B_other4.838
r_mcangle_it4.312
r_mcangle_other4.312
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.539
r_dihedral_angle_2_deg34.512
r_sphericity_bonded24.977
r_dihedral_angle_4_deg14.788
r_dihedral_angle_3_deg14.34
r_dihedral_angle_1_deg5.587
r_long_range_B_refined4.946
r_long_range_B_other4.838
r_mcangle_it4.312
r_mcangle_other4.312
r_scangle_other3.636
r_mcbond_it3.22
r_mcbond_other3.22
r_scbond_it2.901
r_scbond_other2.901
r_rigid_bond_restr1.498
r_angle_refined_deg1.101
r_angle_other_deg0.872
r_chiral_restr0.063
r_bond_refined_d0.007
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 Atoms49304
Nucleic Acid Atoms
Solvent Atoms840
Heterogen Atoms122

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement