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Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (MIT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GB5 PDB entry 3GB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 20% PEG 3350, 0.2M MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.32 71.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.187 α = 90 b = 105.187 β = 90 c = 162.124 γ = 120
Symmetry Space Group P 32 2 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 CCD ADSC QUANTUM 315r 2008-06-08 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.45 50 99.2 0.081 0.081 20 4.7 38478 38170 2
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) Redundancy Number Unique Reflections (All) 1 2.45 2.54 99.3 0.439 0.439 3.7 4.7 3783
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3GB5 2.45 30 36506 36214 1925 99.2 0.145 0.145 0.144 0.1432 0.178 0.1788 RANDOM 38.779
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] 1.88 0.94 1.88 -2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.159 r_dihedral_angle_4_deg 19.385 r_dihedral_angle_1_deg 17.323 r_dihedral_angle_3_deg 16.196 r_scangle_it 5.026 r_scbond_it 3.002 r_angle_refined_deg 2.016 r_mcangle_it 1.736 r_mcbond_it 0.947 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.159 r_dihedral_angle_4_deg 19.385 r_dihedral_angle_1_deg 17.323 r_dihedral_angle_3_deg 16.196 r_scangle_it 5.026 r_scbond_it 3.002 r_angle_refined_deg 2.016 r_mcangle_it 1.736 r_mcbond_it 0.947 r_nbtor_refined 0.32 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.181 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.141 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3550 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing