☰ Navigation Tabs
thyroxine-binding globulin complex with thyroxine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXA PDB ENTRY 1YXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 10MM TRIS-HCL, 50MM NACL, 1MM EDTA PH 7.4, 20% PEG 3350, 0.2M NAF, 5% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.27 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.404 α = 90 b = 88.022 β = 90 c = 124.118 γ = 90
Symmetry Space Group P 21 21 21
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 CCD MIRRORS 2005-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 30.14 93.6 0.2 9.65 13.8 19138 -5 38.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 64.8 0.5 2.24
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 (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 1YXA 2.8 30.14 18166 972 93.6 0.237 0.235 0.2282 0.283 0.2813 RANDOM 8.19
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] -3.34 5.53 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.114 r_dihedral_angle_3_deg 16.015 r_dihedral_angle_4_deg 10.059 r_dihedral_angle_1_deg 5.78 r_mcangle_it 2.372 r_scangle_it 2.168 r_mcbond_it 1.441 r_scbond_it 1.429 r_angle_refined_deg 1.011 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.114 r_dihedral_angle_3_deg 16.015 r_dihedral_angle_4_deg 10.059 r_dihedral_angle_1_deg 5.78 r_mcangle_it 2.372 r_scangle_it 2.168 r_mcbond_it 1.441 r_scbond_it 1.429 r_angle_refined_deg 1.011 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.267 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.184 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5798 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing