2VQE | pdb_00002vqe

Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J5E	PDB ENTRY 1J5E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		SEE WIMBERLY ET AL., NATURE 2000, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.85	74.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 401.998	α = 90
b = 401.998	β = 90
c = 175.648	γ = 90

Symmetry
Space Group	P 41 21 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	MARRESEARCH		2006-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	2.5	50	97.4	0.16	9.7	7.5		587336		2	53.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	97.3		0.77	2.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1J5E	2.5	49.5	487131	24512	99.8	0.257	0.257	0.25	0.283	0.27	RANDOM	61.1

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]
-2.5			-2.5		4.99

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	28.5
c_improper_angle_d	1.64
c_angle_deg	1.5
c_bond_d	0.081
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_na
c_dihedral_angle_d_prot
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	19210
Nucleic Acid Atoms	32723
Solvent Atoms
Heterogen Atoms	312

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNS	phasing