5JYX

Crystal structure of the covalent thioimide intermediate of the archaeosine synthase QueF-Like

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	66 uM preQ0, 17-19% PEG3350, 0.15 M potassium thiocyanate, and 0.05% sodium azide.

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 215.325	α = 90
b = 126.779	β = 102.58
c = 65.083	γ = 90

Symmetry
Space Group	C 1 2 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		2015-05-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97607	SSRL	BL7-1

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	2.74	29	98.7	0.06	25.5	7.6		43893

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	2.75	2.8	98.4		0.597	3	7.6	2172

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.74	108.56	41291	1975	96.34	0.1752	0.1711	0.2588	RANDOM	54.255

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]
0.15		0.13	-0.12		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.435
r_dihedral_angle_4_deg	19.728
r_dihedral_angle_3_deg	17.532
r_dihedral_angle_1_deg	6.675
r_mcangle_it	3.953
r_mcbond_it	2.298
r_mcbond_other	2.298
r_angle_refined_deg	2.149
r_angle_other_deg	1.01
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.435
r_dihedral_angle_4_deg	19.728
r_dihedral_angle_3_deg	17.532
r_dihedral_angle_1_deg	6.675
r_mcangle_it	3.953
r_mcbond_it	2.298
r_mcbond_other	2.298
r_angle_refined_deg	2.149
r_angle_other_deg	1.01
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12191
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	198

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing
HKL-2000	data reduction
PHASER	phasing

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.