7UK3 | pdb_00007uk3

Crystal structure of queuine salvage enzyme DUF2419, wild-type (non-His6x tagged)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7U07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2M Sodium thiocynate, 20% PEG3350, pH 6.9

Crystal Properties
Matthews coefficient	Solvent content
4.65	73.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.159	α = 90
b = 95.159	β = 90
c = 129.32	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	DECTRIS PILATUS 6M		2022-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.3	42	100	0.265	0.279	0.086	3.6	10.3		30413

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	2.3	2.34	99.9		6.599	6.971	2.225	0.309		9.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7U07	2.31	41.24	24343	1317	84.44	0.1518	0.1505	0.16	0.1746	0.18	RANDOM	38.493

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]
-1.14	-0.57		-1.14		3.7

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	43.912
r_dihedral_angle_2_deg	30.46
r_sphericity_bonded	22.855
r_dihedral_angle_3_deg	18.155
r_dihedral_angle_4_deg	18.106
r_dihedral_angle_1_deg	5.447
r_rigid_bond_restr	1.483
r_angle_refined_deg	1.021
r_angle_other_deg	0.783
r_chiral_restr	0.041

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	43.912
r_dihedral_angle_2_deg	30.46
r_sphericity_bonded	22.855
r_dihedral_angle_3_deg	18.155
r_dihedral_angle_4_deg	18.106
r_dihedral_angle_1_deg	5.447
r_rigid_bond_restr	1.483
r_angle_refined_deg	1.021
r_angle_other_deg	0.783
r_chiral_restr	0.041
r_bond_refined_d	0.006
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	2530
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	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 R01GM157729.