9FRW | pdb_00009frw

Yeast 20S proteasome with human beta1i (1-51)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CZ4Yeast 20S proteasome at 2.3 A resolution

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
3.7567.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.43α = 90
b = 301.91β = 112.83
c = 145.53γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-23MSINGLE 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
12.853093.80.0859.43234648
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)
12.852.9597.30.6622.13.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.85302227741172593.870.184840.182570.1880.227430.2299RANDOM65.325
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]
-0.55-4.281.741.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.418
r_dihedral_angle_3_deg14.702
r_dihedral_angle_4_deg14.407
r_dihedral_angle_1_deg6.113
r_long_range_B_refined5.492
r_long_range_B_other5.478
r_mcangle_it3.946
r_mcangle_other3.946
r_scangle_other3.585
r_mcbond_it2.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.418
r_dihedral_angle_3_deg14.702
r_dihedral_angle_4_deg14.407
r_dihedral_angle_1_deg6.113
r_long_range_B_refined5.492
r_long_range_B_other5.478
r_mcangle_it3.946
r_mcangle_other3.946
r_scangle_other3.585
r_mcbond_it2.653
r_mcbond_other2.653
r_scbond_it2.439
r_scbond_other2.437
r_angle_refined_deg1.188
r_angle_other_deg1.06
r_rigid_bond_restr0.349
r_chiral_restr0.035
r_bond_refined_d0.002
r_gen_planes_refined0.002
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49255
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing