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Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI) in complex with 2-guanidino-ethyl-mercaptosuccinic acid (GEMSA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D66 pdb entry 3D66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 277 16-18% PEG 3000, 0.18-0.22mM Na/K-tartrate, 50mM L-glutamate, 50mM L-arginine, 1mM GEMSA, pH 6.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.56 65.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.05 α = 90 b = 161.05 β = 90 c = 138.99 γ = 120
Symmetry Space Group P 31 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 2007-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97320 ESRF ID23-1
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 3.4 49.27 99.6 0.091 11.4 4.9 28920 28900 -3.7
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 3.4 3.58 100 0.63 2.2 5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3D66 3.4 44.09 27424 27424 1472 99.57 0.20043 0.19772 0.25218 0.2551 RANDOM 100.733
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] 4.12 2.06 4.12 -6.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.753 r_dihedral_angle_3_deg 20.197 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_1_deg 8.742 r_angle_refined_deg 1.485 r_scangle_it 1.407 r_angle_other_deg 0.945 r_scbond_it 0.872 r_mcangle_it 0.836 r_mcbond_it 0.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.753 r_dihedral_angle_3_deg 20.197 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_1_deg 8.742 r_angle_refined_deg 1.485 r_scangle_it 1.407 r_angle_other_deg 0.945 r_scbond_it 0.872 r_mcangle_it 0.836 r_mcbond_it 0.471 r_metal_ion_refined 0.353 r_nbd_refined 0.237 r_symmetry_vdw_other 0.207 r_nbtor_refined 0.201 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.168 r_nbtor_other 0.096 r_symmetry_hbond_refined 0.092 r_chiral_restr 0.086 r_mcbond_other 0.059 r_xyhbond_nbd_other 0.017 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9738 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction SCALA data scaling PHASER phasing