5CZ7

Yeast 20S proteasome beta5-T1A beta5-K81R double mutant in complex with Bortezomib, propeptide expressed in cis


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 = 136.09α = 90
b = 301.66β = 113.44
c = 145.51γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-04-12MSINGLE 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
12.53099.60.05617.13.8370111368631
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)
12.52.699.60.4533.5

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 REPLACEMENTTHROUGHOUT1RYP2.5153501991843299.740.198040.197130.21511RANDOM56.871
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]
3.23-0.93-4.811.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.599
r_sphericity_free26.127
r_dihedral_angle_3_deg13.735
r_dihedral_angle_4_deg13.46
r_dihedral_angle_1_deg4.994
r_sphericity_bonded3.845
r_long_range_B_refined2.262
r_long_range_B_other2.189
r_mcangle_it1.741
r_mcangle_other1.741
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.599
r_sphericity_free26.127
r_dihedral_angle_3_deg13.735
r_dihedral_angle_4_deg13.46
r_dihedral_angle_1_deg4.994
r_sphericity_bonded3.845
r_long_range_B_refined2.262
r_long_range_B_other2.189
r_mcangle_it1.741
r_mcangle_other1.741
r_scangle_other1.572
r_mcbond_it1.428
r_mcbond_other1.428
r_scbond_it1.428
r_scbond_other1.428
r_angle_refined_deg0.836
r_angle_other_deg0.676
r_rigid_bond_restr0.628
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
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 Atoms49448
Nucleic Acid Atoms
Solvent Atoms1115
Heterogen Atoms127

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement