4R18

Ligand-induced Lys33-Thr1 crosslinking at subunit beta5 of the yeast 20S proteasome


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, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.58α = 90
b = 300.82β = 113.2
c = 146.29γ = 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
12.43096.90.04417.33.140827822
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)
12.42.597.80.4174

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RYP2.4154082773878632041496.990.1810.178060.177180.19486RANDOM56.74
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]
3.41-0.67-4.791.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.121
r_sphericity_free25.257
r_dihedral_angle_3_deg17.178
r_dihedral_angle_4_deg17.176
r_sphericity_bonded8.08
r_dihedral_angle_1_deg5.801
r_long_range_B_refined2.617
r_long_range_B_other2.504
r_scangle_other1.956
r_scbond_it1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.121
r_sphericity_free25.257
r_dihedral_angle_3_deg17.178
r_dihedral_angle_4_deg17.176
r_sphericity_bonded8.08
r_dihedral_angle_1_deg5.801
r_long_range_B_refined2.617
r_long_range_B_other2.504
r_scangle_other1.956
r_scbond_it1.93
r_scbond_other1.929
r_mcangle_it1.848
r_mcangle_other1.848
r_mcbond_it1.576
r_mcbond_other1.576
r_rigid_bond_restr1.47
r_angle_refined_deg0.976
r_angle_other_deg0.706
r_chiral_restr0.056
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49352
Nucleic Acid Atoms
Solvent Atoms1740
Heterogen Atoms23

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing