5YV5

Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal ribosome recycling factor aABCE1.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YQT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29315% (w/v) PEG 4000, 10% (v/v) 2-propanol, 0.1 M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2946.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.011α = 90
b = 64.731β = 90
c = 147.073γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.119.9897.221.033.18316822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.22

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 REPLACEMENTTHROUGHOUT1YQT2.119.9831682171497.220.196950.194390.24376RANDOM29.331
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.005
r_dihedral_angle_4_deg16.372
r_dihedral_angle_3_deg13.5
r_dihedral_angle_1_deg5.508
r_long_range_B_refined4.13
r_long_range_B_other4.023
r_scangle_other2.212
r_mcangle_it2.016
r_mcangle_other2.015
r_scbond_it1.276
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.005
r_dihedral_angle_4_deg16.372
r_dihedral_angle_3_deg13.5
r_dihedral_angle_1_deg5.508
r_long_range_B_refined4.13
r_long_range_B_other4.023
r_scangle_other2.212
r_mcangle_it2.016
r_mcangle_other2.015
r_scbond_it1.276
r_scbond_other1.276
r_mcbond_it1.157
r_mcbond_other1.157
r_angle_refined_deg1.104
r_angle_other_deg0.713
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4199
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
BALBESphasing