5CGI

Yeast 20S proteasome beta5-G48C mutant in complex with ONX 0914


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 = 136.19α = 90
b = 300.03β = 112.96
c = 145.04γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-05-05MSINGLE 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
12.83098.60.067143.12590882
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)
12.8399.10.4423.1

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 REPLACEMENTTHROUGHOUT1RYP2.8152461331295598.80.1870.1860.206RANDOM66.09
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]
2.96-1.07-7.473.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.335
r_sphericity_free28.752
r_dihedral_angle_4_deg14.78
r_dihedral_angle_3_deg14.472
r_sphericity_bonded5.057
r_dihedral_angle_1_deg4.821
r_long_range_B_refined2.803
r_long_range_B_other2.791
r_mcangle_it2.449
r_mcangle_other2.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.335
r_sphericity_free28.752
r_dihedral_angle_4_deg14.78
r_dihedral_angle_3_deg14.472
r_sphericity_bonded5.057
r_dihedral_angle_1_deg4.821
r_long_range_B_refined2.803
r_long_range_B_other2.791
r_mcangle_it2.449
r_mcangle_other2.449
r_scangle_other2.206
r_mcbond_it1.915
r_mcbond_other1.915
r_scbond_it1.895
r_scbond_other1.895
r_rigid_bond_restr1.17
r_angle_refined_deg0.904
r_angle_other_deg0.745
r_chiral_restr0.05
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 Atoms49300
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms312

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing