4V4I

Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelModelArchivema-ce688entries 1TWT AND 1TWV that were moved from PDB to ModelArchive
in silico modelModelArchivema-cbwe8entries 1TWT AND 1TWV that were moved from PDB to ModelArchive

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.528924-26% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
575.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 507.81α = 90
b = 507.81β = 90
c = 689.52γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 12.3.1ALS12.3.1

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
13.77599.30.1495.44658941.5
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)
13.73.896.60.4674.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 entries 1TWT AND 1TWV3.7130455685113451000.3490.3490.3480.353RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.009
r_mcangle_it35.427
r_mcbond_it25.357
r_dihedral_angle_3_deg17.715
r_dihedral_angle_4_deg16.421
r_scangle_it10.125
r_scbond_it5.208
r_dihedral_angle_1_deg2.795
r_angle_refined_deg1.393
r_symmetry_vdw_refined0.488
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.009
r_mcangle_it35.427
r_mcbond_it25.357
r_dihedral_angle_3_deg17.715
r_dihedral_angle_4_deg16.421
r_scangle_it10.125
r_scbond_it5.208
r_dihedral_angle_1_deg2.795
r_angle_refined_deg1.393
r_symmetry_vdw_refined0.488
r_nbd_refined0.417
r_symmetry_hbond_refined0.366
r_xyhbond_nbd_refined0.326
r_nbtor_refined0.322
r_chiral_restr0.109
r_gen_planes_refined0.015
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26862
Nucleic Acid Atoms64786
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSrefinement
d*TREKdata reduction
CCP4data scaling
CNSphasing