3GB5

Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529320% PEG 3000, 0.1 M Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3247.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.756α = 90
b = 87.756β = 90
c = 62.652γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-04-04SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.653APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
125099.83638236382
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.07994.38.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT250191131911398499.80.1690.1690.1670.189RANDOM32.568
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]
0.380.190.38-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.485
r_dihedral_angle_1_deg16.679
r_dihedral_angle_3_deg14.079
r_dihedral_angle_4_deg11.962
r_scangle_it4.326
r_scbond_it2.803
r_mcangle_it1.606
r_angle_refined_deg1.569
r_mcbond_it1.121
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.485
r_dihedral_angle_1_deg16.679
r_dihedral_angle_3_deg14.079
r_dihedral_angle_4_deg11.962
r_scangle_it4.326
r_scbond_it2.803
r_mcangle_it1.606
r_angle_refined_deg1.569
r_mcbond_it1.121
r_nbtor_refined0.298
r_nbd_refined0.21
r_symmetry_vdw_refined0.196
r_xyhbond_nbd_refined0.143
r_chiral_restr0.121
r_symmetry_hbond_refined0.105
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1479
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing