5FGG

Yeast 20S proteasome beta5-L(-49S)_D17N double mutant in complex with Carfilzomib


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYP 

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 = 134.33α = 90
b = 300.47β = 112.69
c = 144.29γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-12-19MSINGLE 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
12.74097.20.07212.43.2280168
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)
12.72.898.50.5193

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 REPLACEMENTTHROUGHOUT1RYP2.7152661581400997.360.189770.18880.20816RANDOM62.755
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]
4.29-0.6-5.661.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.992
r_sphericity_free29.753
r_dihedral_angle_3_deg13.951
r_dihedral_angle_4_deg13.505
r_sphericity_bonded4.877
r_dihedral_angle_1_deg4.744
r_long_range_B_refined2.715
r_long_range_B_other2.693
r_mcangle_it2.335
r_mcangle_other2.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.992
r_sphericity_free29.753
r_dihedral_angle_3_deg13.951
r_dihedral_angle_4_deg13.505
r_sphericity_bonded4.877
r_dihedral_angle_1_deg4.744
r_long_range_B_refined2.715
r_long_range_B_other2.693
r_mcangle_it2.335
r_mcangle_other2.335
r_scangle_other2.103
r_scbond_it1.849
r_scbond_other1.849
r_mcbond_it1.832
r_mcbond_other1.832
r_rigid_bond_restr1.165
r_angle_refined_deg0.888
r_angle_other_deg0.751
r_chiral_restr0.048
r_bond_refined_d0.004
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 Atoms49303
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms372

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement