4V4I

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


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details 24-26% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

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

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 12.3.1 -- ALS 12.3.1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3.7 75 99.3 0.149 -- -- 5.4 -- 465894 -- 1.5 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.7 3.8 96.6 0.467 -- -- 4.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.71 30.0 -- 0.0 -- 455685 11345 100.0 0.349 0.349 0.348 0.353 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.71 3.805 32511 630 31881 -- -- -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 16.421
r_nbd_refined 0.417
r_scangle_it 10.125
r_dihedral_angle_1_deg 2.795
r_dihedral_angle_3_deg 17.715
r_bond_refined_d 0.011
r_mcbond_it 25.357
r_xyhbond_nbd_refined 0.326
r_scbond_it 5.208
r_chiral_restr 0.109
r_symmetry_hbond_refined 0.366
r_gen_planes_refined 0.015
r_symmetry_vdw_refined 0.488
r_nbtor_refined 0.322
r_angle_refined_deg 1.393
r_dihedral_angle_2_deg 41.009
r_mcangle_it 35.427
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 26862
Nucleic Acid Atoms 64786
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: QUANTUM
CNS refinement
d*TREK data reduction
CCP4 data scaling version: (SCALA)
CNS phasing