3MG8

Structure of yeast 20S open-gate proteasome with Compound 16


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
3.7967.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.333α = 90
b = 299.185β = 113.13
c = 145.667γ = 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
12.595095.60.07311.13.3315407
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)
12.592.6985.90.3272.828297

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 1g0u2.5949.88315315636895.220.2240.2240.252RANDOM43.403
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]
0.18-0.02-0.270.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.626
r_dihedral_angle_3_deg17.257
r_dihedral_angle_4_deg15.882
r_dihedral_angle_1_deg5.752
r_scangle_it1.99
r_angle_refined_deg1.12
r_scbond_it1.113
r_mcangle_it0.89
r_mcbond_it0.462
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.626
r_dihedral_angle_3_deg17.257
r_dihedral_angle_4_deg15.882
r_dihedral_angle_1_deg5.752
r_scangle_it1.99
r_angle_refined_deg1.12
r_scbond_it1.113
r_mcangle_it0.89
r_mcbond_it0.462
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49298
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms126

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction