6HTR

Yeast 20S proteasome with human beta2c (S171G) in complex with 13


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 = 136.36α = 90
b = 300.53β = 113.41
c = 144.81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-06-18MSINGLE 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
12.650970.0719.93317160
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)
12.62.799.30.512

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 REPLACEMENTTHROUGHOUT5CZ42.6152997691577796.610.195260.19370.22473RANDOM67.846
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]
-1.67-1.660.072.21
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.241
r_dihedral_angle_2_deg35.293
r_sphericity_bonded24.341
r_dihedral_angle_3_deg15.845
r_dihedral_angle_4_deg15.218
r_dihedral_angle_1_deg5.826
r_long_range_B_refined5.235
r_long_range_B_other5.188
r_mcangle_it4.647
r_mcangle_other4.647
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.241
r_dihedral_angle_2_deg35.293
r_sphericity_bonded24.341
r_dihedral_angle_3_deg15.845
r_dihedral_angle_4_deg15.218
r_dihedral_angle_1_deg5.826
r_long_range_B_refined5.235
r_long_range_B_other5.188
r_mcangle_it4.647
r_mcangle_other4.647
r_scangle_other4.071
r_mcbond_it3.45
r_mcbond_other3.449
r_scbond_it3.244
r_scbond_other3.244
r_rigid_bond_restr1.284
r_angle_refined_deg1.208
r_angle_other_deg0.945
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms49010
Nucleic Acid Atoms
Solvent Atoms697
Heterogen Atoms184

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement