6O6D

N-terminal domain of translation initiation factor IF-3 from Helicobacter pylori

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.09 M HEPES-NaOH buffer, 1.26 M sodium citrate, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.468	α = 90
b = 56.468	β = 90
c = 55.142	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	ADSC QUANTUM 210r		2019-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9792	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.82	39.48	99.8	0.059	0.063	0.021	0.997	15.5	8.3		8462

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85	99.5		0.934	0.998	0.339	0.819	1.75	7.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.82	39.48	7996	427	99.72	0.1769	0.1752	0.2145	RANDOM	43.994

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]
1.19			1.19		-2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.544
r_dihedral_angle_4_deg	23.324
r_dihedral_angle_3_deg	14.353
r_dihedral_angle_1_deg	5.782
r_angle_refined_deg	1.691
r_angle_other_deg	1.414
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.544
r_dihedral_angle_4_deg	23.324
r_dihedral_angle_3_deg	14.353
r_dihedral_angle_1_deg	5.782
r_angle_refined_deg	1.691
r_angle_other_deg	1.414
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	511
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.