4Y84

Yeast 20S proteasome in complex with N3-A(4,4-F2P)nLL-ep


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYP 

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 = 136.95α = 90
b = 299.9β = 113
c = 145.79γ = 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
12.75097.20.07511.22.9287412287412
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)
12.72.897.40.5742.1

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 REPLACEMENTTHROUGHOUT1RYP2.7152730411437197.360.185580.184650.2034RANDOM63.269
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]
3.11-0.21-7.032.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.687
r_sphericity_free27.704
r_dihedral_angle_4_deg18.927
r_dihedral_angle_3_deg18.859
r_dihedral_angle_1_deg6.448
r_sphericity_bonded5.583
r_long_range_B_refined3.092
r_long_range_B_other3.076
r_mcangle_it2.738
r_mcangle_other2.738
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.687
r_sphericity_free27.704
r_dihedral_angle_4_deg18.927
r_dihedral_angle_3_deg18.859
r_dihedral_angle_1_deg6.448
r_sphericity_bonded5.583
r_long_range_B_refined3.092
r_long_range_B_other3.076
r_mcangle_it2.738
r_mcangle_other2.738
r_scangle_other2.637
r_scbond_it2.56
r_scbond_other2.56
r_mcbond_it2.331
r_mcbond_other2.331
r_rigid_bond_restr2.129
r_angle_refined_deg1.183
r_angle_other_deg0.836
r_chiral_restr0.066
r_bond_refined_d0.006
r_bond_other_d0.003
r_gen_planes_refined0.003
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 Atoms49304
Nucleic Acid Atoms
Solvent Atoms344
Heterogen Atoms273

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement