6HVY

Yeast 20S proteasome in complex with 5 (7- and 6-membered ring)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CZ4 

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 = 136.63α = 90
b = 301.8β = 113.06
c = 145.57γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2014-09-07MSINGLE 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
12.75097.90.07412.53.1290007
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)
12.72.898.60.5522.4

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 REPLACEMENTTHROUGHOUT5CZ42.7152739271441897.480.183270.181450.21774RANDOM61.376
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]
2.72-0.08-3.620.72
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.163
r_dihedral_angle_2_deg34.74
r_sphericity_bonded17.418
r_dihedral_angle_3_deg14.407
r_dihedral_angle_4_deg14.372
r_dihedral_angle_1_deg5.352
r_long_range_B_refined4.319
r_long_range_B_other4.306
r_mcangle_it3.666
r_mcangle_other3.666
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.163
r_dihedral_angle_2_deg34.74
r_sphericity_bonded17.418
r_dihedral_angle_3_deg14.407
r_dihedral_angle_4_deg14.372
r_dihedral_angle_1_deg5.352
r_long_range_B_refined4.319
r_long_range_B_other4.306
r_mcangle_it3.666
r_mcangle_other3.666
r_scangle_other3.426
r_mcbond_it2.723
r_mcbond_other2.723
r_scbond_it2.713
r_scbond_other2.713
r_angle_refined_deg1.056
r_rigid_bond_restr0.99
r_angle_other_deg0.888
r_chiral_restr0.057
r_bond_refined_d0.006
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 Atoms49376
Nucleic Acid Atoms
Solvent Atoms544
Heterogen Atoms218

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing