9QDS | pdb_00009qds

Yeast 20S proteasome mutant: beta1_G128V (b1-propeptide deleted) in complex with Carfilzomib


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
3.7467.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.75α = 90
b = 300.88β = 113.56
c = 145.06γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-12-19MSINGLE 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
12.83096.20.07710.33.1253033
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)
12.82.997.20.462.83

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.8152388251257095.660.174630.17260.18030.211110.2171RANDOM65.563
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]
0.34-0.74-3.282.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.589
r_dihedral_angle_3_deg15.587
r_dihedral_angle_4_deg15.396
r_dihedral_angle_1_deg6.258
r_long_range_B_refined5.663
r_long_range_B_other5.652
r_mcangle_it4.118
r_mcangle_other4.117
r_scangle_other3.879
r_mcbond_it2.807
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.589
r_dihedral_angle_3_deg15.587
r_dihedral_angle_4_deg15.396
r_dihedral_angle_1_deg6.258
r_long_range_B_refined5.663
r_long_range_B_other5.652
r_mcangle_it4.118
r_mcangle_other4.117
r_scangle_other3.879
r_mcbond_it2.807
r_mcbond_other2.806
r_scbond_it2.699
r_scbond_other2.699
r_angle_refined_deg1.302
r_angle_other_deg1.16
r_rigid_bond_restr0.504
r_chiral_restr0.042
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.002
r_gen_planes_other0.002
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49622
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing