4V4J | pdb_00004v4j

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VSA	1VSA, 2OW8. PROTEINS L15, L19, L21, L28 AND L29 FROM PDB ENTRY 2J03.
experimental model	PDB	2OW8	1VSA, 2OW8. PROTEINS L15, L19, L21, L28 AND L29 FROM PDB ENTRY 2J03.
experimental model	PDB	2J03	1VSA, 2OW8. PROTEINS L15, L19, L21, L28 AND L29 FROM PDB ENTRY 2J03.

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.3403	0.351	0.36	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
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