6HWD

Yeast 20S proteasome beta2-G45A mutant in complex with bortezomib


X-RAY DIFFRACTION

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 = 135.48α = 90
b = 300.06β = 113.09
c = 144.86γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2014-06-07MSINGLE 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
12.85098.10.08113255734
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)
12.82.998.90.082.9

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 REPLACEMENTTHROUGHOUT5CZ42.8152413781270497.640.187130.185890.21085RANDOM64.849
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]
2.190.28-4.931.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.859
r_sphericity_free32.149
r_dihedral_angle_3_deg14.498
r_dihedral_angle_4_deg13.811
r_dihedral_angle_1_deg5.827
r_sphericity_bonded5.333
r_long_range_B_refined3.229
r_long_range_B_other3.176
r_mcangle_it2.67
r_mcangle_other2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.859
r_sphericity_free32.149
r_dihedral_angle_3_deg14.498
r_dihedral_angle_4_deg13.811
r_dihedral_angle_1_deg5.827
r_sphericity_bonded5.333
r_long_range_B_refined3.229
r_long_range_B_other3.176
r_mcangle_it2.67
r_mcangle_other2.67
r_scangle_other2.318
r_mcbond_it1.992
r_mcbond_other1.992
r_scbond_it1.911
r_scbond_other1.911
r_rigid_bond_restr1.446
r_angle_refined_deg1.14
r_angle_other_deg0.883
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49378
Nucleic Acid Atoms
Solvent Atoms667
Heterogen Atoms178

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement