4Y8R

Yeast 20S proteasome beta2-H116D mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties
Matthew coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.36α = 90
b = 300.59β = 112.75
c = 143.85γ = 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
12.75097.40.07510.63.1273065273065
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)
12.72.897.40.5592.5

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 REPLACEMENTTHROUGHOUT1RYP2.7152594111365495.160.203960.203020.22201RANDOM59.066
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]
3.61-2.51-5.151.92
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.808
r_dihedral_angle_2_deg34.66
r_dihedral_angle_4_deg14.763
r_dihedral_angle_3_deg14.673
r_dihedral_angle_1_deg5.245
r_sphericity_bonded4.307
r_long_range_B_refined2.297
r_long_range_B_other2.25
r_mcangle_it1.755
r_mcangle_other1.755
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.808
r_dihedral_angle_2_deg34.66
r_dihedral_angle_4_deg14.763
r_dihedral_angle_3_deg14.673
r_dihedral_angle_1_deg5.245
r_sphericity_bonded4.307
r_long_range_B_refined2.297
r_long_range_B_other2.25
r_mcangle_it1.755
r_mcangle_other1.755
r_scangle_other1.674
r_scbond_other1.501
r_scbond_it1.501
r_mcbond_it1.388
r_mcbond_other1.388
r_rigid_bond_restr1.17
r_angle_refined_deg0.864
r_angle_other_deg0.667
r_chiral_restr0.05
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_refined
r_symmetry_metal_ion_other
r_symmetry_vdw_other
r_metal_ion_other
r_metal_ion_refined
r_xyhbond_nbd_other
r_symmetry_hbond_refined
r_nbtor_other
r_scangle_it
r_nbtor_refined
r_nbd_other
r_nbd_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49372
Nucleic Acid Atoms
Solvent Atoms665
Heterogen Atoms23

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement