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Crystal structure of a T325I/T329I/H333Y/H335Q mutant of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI-IIYQ)
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, pH 6.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.5 64.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.46 α = 90 b = 159.46 β = 90 c = 139.18 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 315 2007-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97295 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 2.8 49.03 100 0.067 13.8 4.3 50676 50644 -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 2.8 2.95 100 0.6 2.1 4.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3D66 2.8 49.03 48058 48058 2582 99.97 0.18976 0.18755 0.1939 0.23156 0.2393 RANDOM 57.601
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] 2.53 1.27 2.53 -3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.557 r_dihedral_angle_3_deg 19.436 r_dihedral_angle_4_deg 16.974 r_dihedral_angle_1_deg 8.307 r_scangle_it 2.265 r_angle_refined_deg 1.871 r_scbond_it 1.539 r_mcangle_it 1.119 r_angle_other_deg 1.027 r_mcbond_it 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.557 r_dihedral_angle_3_deg 19.436 r_dihedral_angle_4_deg 16.974 r_dihedral_angle_1_deg 8.307 r_scangle_it 2.265 r_angle_refined_deg 1.871 r_scbond_it 1.539 r_mcangle_it 1.119 r_angle_other_deg 1.027 r_mcbond_it 0.924 r_symmetry_vdw_other 0.275 r_symmetry_vdw_refined 0.253 r_nbd_refined 0.246 r_nbtor_refined 0.209 r_nbd_other 0.206 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.16 r_mcbond_other 0.128 r_chiral_restr 0.108 r_nbtor_other 0.103 r_metal_ion_refined 0.103 r_xyhbond_nbd_other 0.066 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 9747 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction SCALA data scaling PHASER phasing