4Y8O

Yeast 20S proteasome beta7-delta7_Cter mutant in complex with Ac-PAF-ep


X-RAY DIFFRACTION

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 = 136.39α = 90
b = 298.81β = 113.09
c = 146.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-04-12MSINGLE 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
12.75096.40.0882.13283754283754
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)
12.72.8980.4962.1

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 REPLACEMENTTHROUGHOUT1RYP2.7152695661418896.480.20970.20860.23052RANDOM63.463
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]
2.481.09-7.293.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.765
r_sphericity_free31.113
r_dihedral_angle_3_deg15.277
r_dihedral_angle_4_deg14.887
r_sphericity_bonded5.405
r_dihedral_angle_1_deg5.268
r_long_range_B_refined3.047
r_long_range_B_other3.025
r_mcangle_it2.697
r_mcangle_other2.697
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.765
r_sphericity_free31.113
r_dihedral_angle_3_deg15.277
r_dihedral_angle_4_deg14.887
r_sphericity_bonded5.405
r_dihedral_angle_1_deg5.268
r_long_range_B_refined3.047
r_long_range_B_other3.025
r_mcangle_it2.697
r_mcangle_other2.697
r_scangle_other2.369
r_mcbond_it2.077
r_mcbond_other2.077
r_scbond_it1.985
r_scbond_other1.985
r_rigid_bond_restr1.453
r_angle_refined_deg0.944
r_angle_other_deg0.775
r_chiral_restr0.057
r_bond_refined_d0.005
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 Atoms49128
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms153

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement