5LF0

Human 20S proteasome complex with Epoxomicin at 2.4 Angstrom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LE5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52910.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5451.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.07α = 90
b = 202.37β = 90
c = 314.79γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FCRL Transfocator2015-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.9763PETRA III, EMBL c/o DESYP14 (MX2)

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
12.41170.2399.90.1712.29.6262073
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.412.599.60.83

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5LE52.41170.232620731383299.50.1820.1790.229RANDOM65.34
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]
0.7-0.760.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.819
r_dihedral_angle_4_deg16.753
r_dihedral_angle_3_deg15.62
r_long_range_B_refined7.013
r_long_range_B_other7.013
r_dihedral_angle_1_deg6.964
r_scangle_other2.447
r_mcangle_it1.996
r_mcangle_other1.996
r_angle_refined_deg1.522
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.819
r_dihedral_angle_4_deg16.753
r_dihedral_angle_3_deg15.62
r_long_range_B_refined7.013
r_long_range_B_other7.013
r_dihedral_angle_1_deg6.964
r_scangle_other2.447
r_mcangle_it1.996
r_mcangle_other1.996
r_angle_refined_deg1.522
r_scbond_it1.455
r_scbond_other1.455
r_mcbond_it1.178
r_mcbond_other1.178
r_angle_other_deg1.177
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms47874
Nucleic Acid Atoms
Solvent Atoms3173
Heterogen Atoms452

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling