5L5E

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


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 = 136.17α = 90
b = 300.84β = 112.95
c = 145.49γ = 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
12.930980.0889.23.2232919
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)
12.9399.40.4992.5

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 REPLACEMENTTHROUGHOUT5CZ42.9152212731164698.140.191650.18980.22673RANDOM76.117
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]
4.770.63-7.371.71
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.292
r_dihedral_angle_2_deg34.443
r_sphericity_bonded18.419
r_dihedral_angle_4_deg14.486
r_dihedral_angle_3_deg14.281
r_long_range_B_refined5.254
r_long_range_B_other5.253
r_dihedral_angle_1_deg4.904
r_mcangle_it4.632
r_mcangle_other4.632
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.292
r_dihedral_angle_2_deg34.443
r_sphericity_bonded18.419
r_dihedral_angle_4_deg14.486
r_dihedral_angle_3_deg14.281
r_long_range_B_refined5.254
r_long_range_B_other5.253
r_dihedral_angle_1_deg4.904
r_mcangle_it4.632
r_mcangle_other4.632
r_scangle_other4.285
r_mcbond_it3.426
r_mcbond_other3.426
r_scbond_it3.399
r_scbond_other3.398
r_angle_refined_deg0.914
r_rigid_bond_restr0.912
r_angle_other_deg0.79
r_chiral_restr0.049
r_bond_refined_d0.005
r_bond_other_d0.003
r_gen_planes_refined0.003
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 Atoms153
Heterogen Atoms347

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement