8DL3 | pdb_00008dl3

Crystal structure of the human queuine salvage enzyme DUF2419, complexed with queuine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2M NaCl, 25% PEG3350, 0.1M Bis-Tris, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
1.95	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.726	α = 90
b = 136.759	β = 90.33
c = 52.606	γ = 90

Symmetry
Space Group	P 1 21 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		2022-06-25	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	2.25	45	97.9	0.226	0.245	0.095	4.1	6.5		27661

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	2.25	2.29	94.5		1.516	1.678	0.705	0.478		5.2

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	7UGK	2.26	42.76	24766	1234	91.51	0.1587	0.1556	0.2221	0.1554	RANDOM	31.754

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]
1.25		0.38	-1.07		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.456
r_dihedral_angle_2_deg	30.707
r_dihedral_angle_4_deg	20.844
r_dihedral_angle_3_deg	16.598
r_sphericity_bonded	14.465
r_dihedral_angle_1_deg	6.287
r_rigid_bond_restr	1.227
r_angle_refined_deg	1.205
r_angle_other_deg	0.863
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5500
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	40

Software

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