4Y6A

Yeast 20S proteasome beta2-H114D mutant in complex with Ac-PAD-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, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.77α = 90
b = 302.73β = 113.19
c = 145.98γ = 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
12.65096.40.074123321495321495
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)
12.62.796.20.5282.4

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 REPLACEMENTTHROUGHOUT1RYP2.6153054201607596.50.218050.21730.23248RANDOM57.842
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]
2.8-0.18-4.741.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.219
r_sphericity_free33.01
r_dihedral_angle_3_deg14.227
r_dihedral_angle_4_deg13.886
r_dihedral_angle_1_deg5.035
r_sphericity_bonded4.619
r_long_range_B_refined2.556
r_long_range_B_other2.482
r_mcangle_it2.033
r_mcangle_other2.033
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.219
r_sphericity_free33.01
r_dihedral_angle_3_deg14.227
r_dihedral_angle_4_deg13.886
r_dihedral_angle_1_deg5.035
r_sphericity_bonded4.619
r_long_range_B_refined2.556
r_long_range_B_other2.482
r_mcangle_it2.033
r_mcangle_other2.033
r_scangle_other1.872
r_mcbond_it1.619
r_mcbond_other1.619
r_scbond_it1.619
r_scbond_other1.618
r_rigid_bond_restr1.091
r_angle_refined_deg0.893
r_angle_other_deg0.736
r_chiral_restr0.051
r_bond_refined_d0.005
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49372
Nucleic Acid Atoms
Solvent Atoms788
Heterogen Atoms63

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement