4V4J

Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	298	Buffer conditions: 25 mM K-HEPES (pH 7.5), 12.5 mM Na-cacodylate pH 5.5, 2.5 mM Tris-HCl (pH 7.5), 80 mM NH_4 Cl, 80 mM KCl, 11 mM MgCl_2, 6.5 mM Thermine HCl and 0.2 M KSCN. Crystallization by the hanging drop method over 26-30% MPD in the above buffer mix, using 2 uL of ribosome complex mixed with 2 uL of well mixture on siliconized cover slips, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.454	72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 507.21	α = 90
b = 507.21	β = 90
c = 692.51	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2004-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	0.9835	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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
1	3.83	78	82	0.15				354761

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1VSA, 2OW8. PROTEINS L15, L19, L21, L28 AND L29 FROM PDB ENTRY 2J03.	3.83	30	346189	10068	81.68	0.327	0.327	0.351	RANDOM

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]
-0.05			-0.05		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.383
r_dihedral_angle_3_deg	18.93
r_dihedral_angle_4_deg	15.665
r_dihedral_angle_1_deg	3.429
r_angle_refined_deg	1.237
r_symmetry_vdw_refined	0.41
r_nbd_refined	0.316
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.277
r_xyhbond_nbd_refined	0.227

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.383
r_dihedral_angle_3_deg	18.93
r_dihedral_angle_4_deg	15.665
r_dihedral_angle_1_deg	3.429
r_angle_refined_deg	1.237
r_symmetry_vdw_refined	0.41
r_nbd_refined	0.316
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.277
r_xyhbond_nbd_refined	0.227
r_chiral_restr	0.082
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26862
Nucleic Acid Atoms	64786
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CNS	refinement
d*TREK	data reduction
SCALA	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.