3MG7

Structure of yeast 20S open-gate proteasome with Compound 8


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 mM MES, 40 mM MgOAc, 15% 2-methyl-2,4-pentanediol (MPD), 10 mM EDTA, pH 7.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
3.7867.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.017α = 90
b = 300.379β = 113.73
c = 145.811γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMAR CCD 165 mmMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

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
12.785097.20.12383.7257519
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)
12.782.985.70.4423.322640

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 REPLACEMENTTHROUGHOUTpdb entry 1g0u2.7848.68256472519195.840.2180.2170.259RANDOM58.954
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]
0.02-0.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.481
r_dihedral_angle_3_deg18.038
r_dihedral_angle_4_deg15.853
r_dihedral_angle_1_deg5.791
r_mcangle_it1.762
r_angle_refined_deg1.14
r_mcbond_it1.043
r_scangle_it0.777
r_scbond_it0.489
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.481
r_dihedral_angle_3_deg18.038
r_dihedral_angle_4_deg15.853
r_dihedral_angle_1_deg5.791
r_mcangle_it1.762
r_angle_refined_deg1.14
r_mcbond_it1.043
r_scangle_it0.777
r_scbond_it0.489
r_nbtor_refined0.302
r_symmetry_vdw_refined0.23
r_nbd_refined0.207
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.137
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49298
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms122

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction