7ULC

Crystal structure of queuine salvage enzyme DUF2419 mutant D231N, in complex with queuosine-5'-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.1 M Sodium malonate, 0.1 M HEPES, 0.5% (v/v) Jaffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
358.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.254α = 90
b = 106.254β = 90
c = 157.927γ = 90
Symmetry
Space GroupP 41 21 2

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
11.995099.90.1730.1790.0434.516.862834
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)
11.992.0299.43.5663.7551.1570.1919.9

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT7U071.9947.5654109281790.990.14510.14370.1715RANDOM32.533
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]
-0.19-0.190.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.189
r_sphericity_free25.582
r_sphericity_bonded19.831
r_dihedral_angle_4_deg18.315
r_dihedral_angle_3_deg15.076
r_dihedral_angle_1_deg5.772
r_rigid_bond_restr2.253
r_angle_refined_deg1.23
r_angle_other_deg0.948
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.189
r_sphericity_free25.582
r_sphericity_bonded19.831
r_dihedral_angle_4_deg18.315
r_dihedral_angle_3_deg15.076
r_dihedral_angle_1_deg5.772
r_rigid_bond_restr2.253
r_angle_refined_deg1.23
r_angle_other_deg0.948
r_chiral_restr0.069
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 Atoms5027
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms73

Software

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