3FOZ | pdb_00003foz

Structure of E. coli Isopentenyl-tRNA transferase in complex with E. coli tRNA(Phe)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D3Q	3D3Q, 1TTT
experimental model	PDB	1TTT	3D3Q, 1TTT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG 4K 15%, 0.2M CaCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.24	α = 90
b = 91.26	β = 90
c = 152.36	γ = 90

Symmetry
Space Group	P 21 21 21

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 325 mm CCD	Double crystal monochromator, Si(111)	2008-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	0.97	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	78.29	99.8	0.097	6.8	6.5	43836	43749	-3	-3	51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	100		0.493	2.14

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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 (All)	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	3D3Q, 1TTT	2.5	30	-3	43779	40403	2133	97.16	0.24517	0.24517	0.24389	0.24	0.26822	0.29	RANDOM	22.657

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]
0.3			1.46		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.731
r_dihedral_angle_4_deg	17.201
r_dihedral_angle_3_deg	16.788
r_mcangle_it	6.154
r_dihedral_angle_1_deg	5.849
r_scangle_it	5.707
r_mcbond_it	4.415
r_scbond_it	4.344
r_mcbond_other	1.369
r_angle_refined_deg	1.279

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.731
r_dihedral_angle_4_deg	17.201
r_dihedral_angle_3_deg	16.788
r_mcangle_it	6.154
r_dihedral_angle_1_deg	5.849
r_scangle_it	5.707
r_mcbond_it	4.415
r_scbond_it	4.344
r_mcbond_other	1.369
r_angle_refined_deg	1.279
r_angle_other_deg	0.875
r_chiral_restr	0.059
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4783
Nucleic Acid Atoms	3055
Solvent Atoms	73
Heterogen Atoms	22

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.