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Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and di-iodotyrosine (DIT)
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 5.5 293 0.2M Ammonium acetate, 45% 2-Methyl-2,4-pentanediol, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.61 α = 90 b = 112.567 β = 89.92 c = 189.253 γ = 90
Symmetry Space Group P 1 21 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 2008-04-04 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 2.6 50 97.1 0.086 0.086 9.7 2.6 62935 62878 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 92.9 0.295 2.4 2.5 5984
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2.61 30 62878 3202 96.82 0.185 0.185 0.181 0.1822 0.264 0.2636 RANDOM 35.532
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] -1.13 -0.16 -4.05 5.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.104 r_dihedral_angle_3_deg 20.523 r_dihedral_angle_4_deg 19.877 r_dihedral_angle_1_deg 7.36 r_scangle_it 3.693 r_scbond_it 2.338 r_angle_refined_deg 1.926 r_mcangle_it 1.502 r_mcbond_it 0.832 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.104 r_dihedral_angle_3_deg 20.523 r_dihedral_angle_4_deg 19.877 r_dihedral_angle_1_deg 7.36 r_scangle_it 3.693 r_scbond_it 2.338 r_angle_refined_deg 1.926 r_mcangle_it 1.502 r_mcbond_it 0.832 r_nbtor_refined 0.324 r_nbd_refined 0.251 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.137 r_symmetry_hbond_refined 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14232 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 378
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