1YAR

Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PMAPDB entry 1PMA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.22730.1M Na-citrate/phosphate buffer, 0.2M Lithium Sulfate, 15% PEG-1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
3.463

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 254.874α = 90
b = 127.512β = 92.45
c = 181.182γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.283NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.92097.40.0630.063105442007
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)
11.91.9795.80.4972.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1PMA1.947.3442001440656134597.240.181960.181960.181850.21624RANDOM31.532
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.69
r_dihedral_angle_4_deg14.903
r_dihedral_angle_3_deg14.644
r_dihedral_angle_1_deg5.807
r_scangle_it3.898
r_scbond_it2.472
r_mcangle_it1.51
r_angle_refined_deg1.271
r_mcbond_it0.973
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.69
r_dihedral_angle_4_deg14.903
r_dihedral_angle_3_deg14.644
r_dihedral_angle_1_deg5.807
r_scangle_it3.898
r_scbond_it2.472
r_mcangle_it1.51
r_angle_refined_deg1.271
r_mcbond_it0.973
r_nbtor_refined0.3
r_nbd_refined0.209
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.161
r_symmetry_hbond_refined0.149
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms34692
Nucleic Acid Atoms
Solvent Atoms3470
Heterogen Atoms147

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing