5ZCY

Crystal structure of archaeal translation initiation factor 1 at 1.5 Angstroms resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	0.2M Lithium Nitrate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.58	α = 90
b = 53.58	β = 90
c = 56.94	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HF	2017-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.5	35.97	98.1	0.054	0.056	0.017	1	23.4	11		14801

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	1.5	1.52	95.9		0.514	0.54	0.165	0.915		10.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4MO0	1.5	35.97	14100	686	98.14	0.1753	0.1738	0.2046	RANDOM	19.198

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]
-0.02	-0.01		-0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.449
r_dihedral_angle_4_deg	12.189
r_dihedral_angle_3_deg	11.61
r_dihedral_angle_1_deg	6.112
r_angle_refined_deg	2.578
r_angle_other_deg	1.098
r_chiral_restr	0.159
r_bond_refined_d	0.028
r_gen_planes_refined	0.011
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.449
r_dihedral_angle_4_deg	12.189
r_dihedral_angle_3_deg	11.61
r_dihedral_angle_1_deg	6.112
r_angle_refined_deg	2.578
r_angle_other_deg	1.098
r_chiral_restr	0.159
r_bond_refined_d	0.028
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	671
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	7

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

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 R01GM133198.