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Crystal structure of thyroxine-binding globulin complexed with mefenamic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RIV PDB ENTRY 2RIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 20% PEG3350, PH 5.4
Crystal Properties Matthews coefficient Solvent content 2.35 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.835 α = 90 b = 41.624 β = 90 c = 56.188 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2007-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.09 21.97 98.2 0.09 14.5 5.2 24692 2
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 2.09 2.21 88.5 0.32 3.3 3.3
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 2RIV 2.09 86.39 23353 1254 99.49 0.21284 0.21038 0.219 0.25957 0.2679 RANDOM 32.786
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] -0.5 3.2 -2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.172 r_dihedral_angle_3_deg 14.074 r_dihedral_angle_4_deg 14.03 r_dihedral_angle_1_deg 6.317 r_scangle_it 2.698 r_scbond_it 1.69 r_angle_refined_deg 1.258 r_mcangle_it 1.172 r_angle_other_deg 0.904 r_mcbond_it 0.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.172 r_dihedral_angle_3_deg 14.074 r_dihedral_angle_4_deg 14.03 r_dihedral_angle_1_deg 6.317 r_scangle_it 2.698 r_scbond_it 1.69 r_angle_refined_deg 1.258 r_mcangle_it 1.172 r_angle_other_deg 0.904 r_mcbond_it 0.629 r_mcbond_other 0.122 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 2928 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling PHASER phasing