3MG6

Structure of yeast 20S open-gate proteasome with Compound 6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G0UPDB ENTRY 1g0u

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
Matthews coefficientSolvent content
3.8167.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.253α = 90
b = 299.646β = 113.67
c = 145.785γ = 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
12.6149.0796.30.09211.17.1315914
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)
12.62.6976.90.3533.325170

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 1g0u2.650314176318995.410.2150.2150.249RANDOM55.262
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]
2.64-0.45-4.621.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.967
r_dihedral_angle_3_deg18.431
r_dihedral_angle_4_deg17.102
r_dihedral_angle_1_deg6.263
r_scangle_it2.341
r_scbond_it1.413
r_angle_refined_deg1.309
r_mcangle_it1.08
r_mcbond_it0.597
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.967
r_dihedral_angle_3_deg18.431
r_dihedral_angle_4_deg17.102
r_dihedral_angle_1_deg6.263
r_scangle_it2.341
r_scbond_it1.413
r_angle_refined_deg1.309
r_mcangle_it1.08
r_mcbond_it0.597
r_nbtor_refined0.306
r_symmetry_vdw_refined0.262
r_nbd_refined0.228
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_refined0.162
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49298
Nucleic Acid Atoms
Solvent Atoms858
Heterogen Atoms120

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction