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Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KWM PDB entry 1KWM
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, 50 mM L-arginine, pH 6.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.61 65.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.74 α = 90 b = 161.74 β = 90 c = 139.45 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 2007-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.26206 ESRF ID29
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 3.1 49.51 100 0.105 13.9 8.6 38621 38593 -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 3.1 3.27 100 0.833 2.6 8.7
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 1KWM 3.1 49.51 36638 36638 1953 99.99 0.20621 0.20442 0.2094 0.24038 0.2396 RANDOM 80.939
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] 3.98 1.99 3.98 -5.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.063 r_dihedral_angle_3_deg 17.734 r_dihedral_angle_4_deg 17.174 r_dihedral_angle_1_deg 10.449 r_scangle_it 2.369 r_angle_refined_deg 1.751 r_scbond_it 1.58 r_mcangle_it 1.198 r_angle_other_deg 1.099 r_mcbond_it 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.063 r_dihedral_angle_3_deg 17.734 r_dihedral_angle_4_deg 17.174 r_dihedral_angle_1_deg 10.449 r_scangle_it 2.369 r_angle_refined_deg 1.751 r_scbond_it 1.58 r_mcangle_it 1.198 r_angle_other_deg 1.099 r_mcbond_it 0.959 r_symmetry_vdw_other 0.342 r_symmetry_vdw_refined 0.31 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.225 r_nbd_other 0.21 r_xyhbond_nbd_refined 0.208 r_nbtor_refined 0.204 r_mcbond_other 0.126 r_xyhbond_nbd_other 0.102 r_chiral_restr 0.098 r_nbtor_other 0.094 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_metal_ion_refined 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 9735 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction SCALA data scaling PHASER phasing