6G7F

Yeast 20S proteasome in complex with Cystargolide B


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 MM MGAC2, 13% MPD, PH 6.8
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.74α = 90
b = 301.97β = 112.95
c = 143.62γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-02-10MSINGLE 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
12.73096.70.06410.882.9278843
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)
12.72.898.80.5152

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 REPLACEMENTTHROUGHOUT5CZ42.7152633581386196.210.189280.187730.21435RANDOM76.987
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]
1.88-2.8-4.643.78
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.064
r_dihedral_angle_2_deg35.176
r_dihedral_angle_3_deg14.469
r_dihedral_angle_4_deg13.814
r_sphericity_bonded6.386
r_dihedral_angle_1_deg5.777
r_long_range_B_refined3.922
r_long_range_B_other3.82
r_mcangle_it3.279
r_mcangle_other3.279
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.064
r_dihedral_angle_2_deg35.176
r_dihedral_angle_3_deg14.469
r_dihedral_angle_4_deg13.814
r_sphericity_bonded6.386
r_dihedral_angle_1_deg5.777
r_long_range_B_refined3.922
r_long_range_B_other3.82
r_mcangle_it3.279
r_mcangle_other3.279
r_scangle_other2.903
r_mcbond_it2.525
r_mcbond_other2.525
r_scbond_it2.443
r_scbond_other2.443
r_angle_refined_deg1.135
r_angle_other_deg0.875
r_rigid_bond_restr0.714
r_chiral_restr0.065
r_bond_refined_d0.007
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 Atoms49333
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing