3JRM

Crystal structure of archaeal 20S proteasome in complex with mutated P26 activator


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YARPDB ENTRY 1YAR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6294pH 5.6, PEG 1000, Sodium phosphate citrate, LiSo4, Imidazole, VAPOR DIFFUSION, Hanging Drop, temperature 294K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.8757.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 255.075α = 90
b = 126.363β = 92.54
c = 180.781γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

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
12.93098.70.1396.75.4126445
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)
2.9398.10.5914.8

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 1YAR2.929.82122666251698.620.202040.201410.2334RANDOM32.39
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]
-1.25-2.771.08-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.092
r_dihedral_angle_3_deg17.499
r_dihedral_angle_4_deg13.226
r_dihedral_angle_1_deg6.536
r_scangle_it2.904
r_scbond_it1.616
r_angle_refined_deg1.371
r_mcangle_it1.047
r_angle_other_deg0.932
r_mcbond_it0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.092
r_dihedral_angle_3_deg17.499
r_dihedral_angle_4_deg13.226
r_dihedral_angle_1_deg6.536
r_scangle_it2.904
r_scbond_it1.616
r_angle_refined_deg1.371
r_mcangle_it1.047
r_angle_other_deg0.932
r_mcbond_it0.51
r_mcbond_other0.095
r_chiral_restr0.074
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms35035
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACphasing