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Structure of human activated thrombin-activatable fibrinolysis inhibitor, TAFIa, in complex with tick-derived funnelin inhibitor, TCI.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M KBr, 0.1M cacodylate, 15% PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.66 73.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.18 α = 90 b = 157.18 β = 90 c = 57.07 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 2001-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 46.2 99.9 0.109 0.109 11.4 6.8 28269 28241 64.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.64 100 0.628 0.628 3.2 6.7
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 (All) 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 3d4u 2.5 46.18 27517 27500 739 99.94 0.18584 0.18584 0.18504 0.1886 0.21618 0.2199 RANDOM 31.821
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] 0.83 0.41 0.83 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.66 r_dihedral_angle_3_deg 16.371 r_dihedral_angle_4_deg 16.278 r_dihedral_angle_1_deg 6.51 r_scangle_it 2.491 r_scbond_it 1.659 r_angle_refined_deg 1.28 r_mcangle_it 1.099 r_angle_other_deg 0.86 r_mcbond_it 0.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.66 r_dihedral_angle_3_deg 16.371 r_dihedral_angle_4_deg 16.278 r_dihedral_angle_1_deg 6.51 r_scangle_it 2.491 r_scbond_it 1.659 r_angle_refined_deg 1.28 r_mcangle_it 1.099 r_angle_other_deg 0.86 r_mcbond_it 0.601 r_mcbond_other 0.167 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3066 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 36
Software Software Software Name Purpose ProDC data collection AMoRE phasing REFMAC refinement XDS data reduction SCALA data scaling