5LF7

Human 20S proteasome complex with Ixazomib at 2.0 Angstrom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LE5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52910.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5451.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.41α = 90
b = 202.61β = 90
c = 314.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FCRL Transfocator2015-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.9763PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12170.3399.60.099114.66.6459122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.05298.30.291

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5LE52170.334591222401899.60.177360.175490.21334RANDOM52.716
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]
3.38-0.27-3.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.427
r_dihedral_angle_4_deg18.529
r_dihedral_angle_3_deg15.755
r_long_range_B_refined9.853
r_long_range_B_other9.853
r_dihedral_angle_1_deg7.281
r_scangle_other3.275
r_scbond_it2.27
r_scbond_other2.269
r_mcangle_it2.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.427
r_dihedral_angle_4_deg18.529
r_dihedral_angle_3_deg15.755
r_long_range_B_refined9.853
r_long_range_B_other9.853
r_dihedral_angle_1_deg7.281
r_scangle_other3.275
r_scbond_it2.27
r_scbond_other2.269
r_mcangle_it2.229
r_mcangle_other2.229
r_angle_refined_deg1.938
r_angle_other_deg1.401
r_mcbond_it1.361
r_mcbond_other1.36
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.007
r_gen_planes_other0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms48004
Nucleic Acid Atoms
Solvent Atoms3595
Heterogen Atoms211

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling