8OHZ

Yeast 20S proteasome in complex with a photoswitchable cepafungin derivative (transCep1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FZC20S yeast proteasome in complex with cepafungin I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
3.766.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.51α = 90
b = 300.79β = 113.41
c = 144.77γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-28MSINGLE 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
12.653095.90.0612.43294565
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)
12.652.7595.90.65523.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.653027968714721960.181720.179560.22233RANDOM76.385
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]
0.06-0.720.79-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.835
r_dihedral_angle_4_deg18.215
r_dihedral_angle_3_deg17.934
r_long_range_B_refined7.224
r_long_range_B_other7.221
r_dihedral_angle_1_deg6.959
r_mcangle_it5.581
r_mcangle_other5.581
r_scangle_other5.382
r_mcbond_it3.873
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.835
r_dihedral_angle_4_deg18.215
r_dihedral_angle_3_deg17.934
r_long_range_B_refined7.224
r_long_range_B_other7.221
r_dihedral_angle_1_deg6.959
r_mcangle_it5.581
r_mcangle_other5.581
r_scangle_other5.382
r_mcbond_it3.873
r_mcbond_other3.873
r_scbond_it3.806
r_scbond_other3.806
r_angle_refined_deg1.237
r_angle_other_deg1.206
r_rigid_bond_restr1
r_chiral_restr0.042
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49376
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms182

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing