4V9K | pdb_00004v9k

70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F1E	PDB Entries 3F1E , 3F1F , 2WRI , 2WRJ
experimental model	PDB	3F1F	PDB Entries 3F1E , 3F1F , 2WRI , 2WRJ
experimental model	PDB	2WRI	PDB Entries 3F1E , 3F1F , 2WRI , 2WRJ
experimental model	PDB	2WRJ	PDB Entries 3F1E , 3F1F , 2WRI , 2WRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				2.9% PEG 20K, 2.8% PPG P400, 5.1% MME 550, KSCN 200 mM, TRIS ACETATE 100mM

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 306.009	α = 90
b = 673.491	β = 92.69
c = 351.984	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 300 mm CCD		2012-06-07	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2012-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03322	APS	23-ID-D
2	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.116	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2	3.497	351.598				770789	2605789	2	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	PDB Entries 3F1E , 3F1F , 2WRI , 2WRJ	3.5	40	2	770789	2605789	38147		0.262	0.262	0.2699	0.309	0.3102	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]

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.07
c_bond_d	0.042
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24442
Nucleic Acid Atoms	34612
Solvent Atoms
Heterogen Atoms	33

Software

Software
Software Name	Purpose
XDS	data scaling
PHASER	phasing
CNS	refinement
XDS	data reduction
SCALA	data scaling