1RYP

CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST AT 2.4 ANGSTROMS RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.9pH 6.9
Crystal Properties
Matthews coefficientSolvent content
3.5365.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.49α = 90
b = 300.7β = 112.89
c = 144.42γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90IMAGE PLATEMARRESEARCH1997-06-09M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/DESY, HAMBURGBW6

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
11.95093.60.08122.97781182
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)
1.9793.60.48721.8

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONPDB ENTRY 1PMA1.95027521013740890.50.2860.2860.3336.4
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]
-4.44.513.9-2.5
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.1
x_scangle_it6.7
x_mcangle_it4.6
x_scbond_it4.6
x_mcbond_it3.2
x_angle_deg1.8
x_improper_angle_d1.34
x_bond_d0.011
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.1
x_scangle_it6.7
x_mcangle_it4.6
x_scbond_it4.6
x_mcbond_it3.2
x_angle_deg1.8
x_improper_angle_d1.34
x_bond_d0.011
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49676
Nucleic Acid Atoms
Solvent Atoms2928
Heterogen Atoms20

Software

Software
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling
X-PLORphasing