3UN4

Yeast 20S proteasome in complex with PR-957 (morpholine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYPpdb entry 1RYP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8293100 mM MES, 12% MPD, 20 mM MgAc2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6866.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.41α = 90
b = 300.78β = 112.75
c = 143.82γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-02-02MSINGLE 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
13.43098.10.1438.214437614163322

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1RYP3.415141632134550708298.290.180860.178850.21948RANDOM80.525
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]
3.86-2.13-8.883.38
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.533
r_dihedral_angle_2_deg36.691
r_dihedral_angle_4_deg13.826
r_dihedral_angle_3_deg13.737
r_sphericity_bonded10.839
r_dihedral_angle_1_deg4.268
r_rigid_bond_restr1.302
r_angle_refined_deg0.899
r_chiral_restr0.059
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.533
r_dihedral_angle_2_deg36.691
r_dihedral_angle_4_deg13.826
r_dihedral_angle_3_deg13.737
r_sphericity_bonded10.839
r_dihedral_angle_1_deg4.268
r_rigid_bond_restr1.302
r_angle_refined_deg0.899
r_chiral_restr0.059
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49538
Nucleic Acid Atoms
Solvent Atoms1322
Heterogen Atoms252

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing