4Y8N

Yeast 20S proteasome beta7-delta7_Cter mutant in complex with Ac-PAE-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 = 136.41α = 90
b = 301.59β = 112.89
c = 145.62γ = 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
12.65095.40.06512.72.9315914315914
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)
12.62.797.20.5622.3

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 REPLACEMENTTHROUGHOUT1RYP2.6153001171579695.460.198110.197210.21506RANDOM64.522
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]
3.430.4-7.462.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.622
r_sphericity_free29.855
r_dihedral_angle_3_deg14.738
r_dihedral_angle_4_deg14.619
r_dihedral_angle_1_deg5.145
r_sphericity_bonded4.725
r_long_range_B_refined2.638
r_long_range_B_other2.593
r_mcangle_it2.185
r_mcangle_other2.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.622
r_sphericity_free29.855
r_dihedral_angle_3_deg14.738
r_dihedral_angle_4_deg14.619
r_dihedral_angle_1_deg5.145
r_sphericity_bonded4.725
r_long_range_B_refined2.638
r_long_range_B_other2.593
r_mcangle_it2.185
r_mcangle_other2.185
r_scangle_other2.001
r_scbond_it1.74
r_scbond_other1.74
r_mcbond_it1.711
r_mcbond_other1.711
r_rigid_bond_restr1.138
r_angle_refined_deg0.888
r_angle_other_deg0.718
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms49226
Nucleic Acid Atoms
Solvent Atoms611
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing