5AH5

Crystal structure of the ternary complex of Agrobacterium radiobacter K84 agnB2 LeuRS-tRNA-LeuAMS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BTE	PDB ENTRIES 2BTE, 4AS1
experimental model	PDB	4AS1	PDB ENTRIES 2BTE, 4AS1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1 M MES PH 6.5, 0.2 M AMMONIUM SULFATE, 27 % PEG 5000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.9	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.91	α = 90
b = 50.32	β = 93.48
c = 170.52	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315r		2011-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.1	48.6	99.4	0.08	10.6	3.7		160330		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	2.1	2.15	99.6		0.76	2.1	3.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 2BTE, 4AS1	2.1	48.58	160330	8487	99.46	0.19634	0.19416	0.23732	RANDOM	50.507

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]
0.16		-0.79			-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.35
r_dihedral_angle_4_deg	17.687
r_dihedral_angle_3_deg	15.711
r_long_range_B_refined	9.179
r_long_range_B_other	9.164
r_dihedral_angle_1_deg	7.705
r_scangle_other	7.005
r_mcangle_it	5.798
r_mcangle_other	5.798
r_scbond_it	4.663
r_scbond_other	4.644
r_mcbond_it	4.058
r_mcbond_other	4.058
r_angle_refined_deg	1.736
r_angle_other_deg	1.137
r_chiral_restr	0.112
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12364
Nucleic Acid Atoms	3423
Solvent Atoms	871
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing