7UK3

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7U07 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2M Sodium thiocynate, 20% PEG3350, pH 6.9
Crystal Properties
Matthews coefficientSolvent content
4.6573.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.159α = 90
b = 95.159β = 90
c = 129.32γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3421000.2650.2790.0863.610.330413
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)RedundancyNumber Unique Reflections (All)
12.32.3499.96.5996.9712.2250.3099.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7U072.3141.2424343131784.440.15180.15050.1746RANDOM38.493
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]
-1.14-0.57-1.143.7
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.912
r_dihedral_angle_2_deg30.46
r_sphericity_bonded22.855
r_dihedral_angle_3_deg18.155
r_dihedral_angle_4_deg18.106
r_dihedral_angle_1_deg5.447
r_rigid_bond_restr1.483
r_angle_refined_deg1.021
r_angle_other_deg0.783
r_chiral_restr0.041
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.912
r_dihedral_angle_2_deg30.46
r_sphericity_bonded22.855
r_dihedral_angle_3_deg18.155
r_dihedral_angle_4_deg18.106
r_dihedral_angle_1_deg5.447
r_rigid_bond_restr1.483
r_angle_refined_deg1.021
r_angle_other_deg0.783
r_chiral_restr0.041
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2530
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing