3GFD

Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (MIT)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GB5PDB entry 3GB5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429320% PEG 3350, 0.2M MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.3271.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.187α = 90
b = 105.187β = 90
c = 162.124γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-06-08SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9795APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
12.455099.20.0810.081204.738478381702
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.5499.30.4390.4393.74.73783

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3GB52.45303650636214192599.20.1450.1450.1440.178RANDOM38.779
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]
1.880.941.88-2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.159
r_dihedral_angle_4_deg19.385
r_dihedral_angle_1_deg17.323
r_dihedral_angle_3_deg16.196
r_scangle_it5.026
r_scbond_it3.002
r_angle_refined_deg2.016
r_mcangle_it1.736
r_mcbond_it0.947
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.159
r_dihedral_angle_4_deg19.385
r_dihedral_angle_1_deg17.323
r_dihedral_angle_3_deg16.196
r_scangle_it5.026
r_scbond_it3.002
r_angle_refined_deg2.016
r_mcangle_it1.736
r_mcbond_it0.947
r_nbtor_refined0.32
r_nbd_refined0.236
r_xyhbond_nbd_refined0.181
r_symmetry_vdw_refined0.171
r_symmetry_hbond_refined0.158
r_chiral_restr0.141
r_bond_refined_d0.019
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3550
Nucleic Acid Atoms
Solvent Atoms540
Heterogen Atoms108

Software

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