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Crystal structure of the C-terminal domain of human TNC in complex with Adhiron 52
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291.15 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M sodium formate, 0.02 M ammonium acetate,
0.02 M trisodium citrate, 0.02 M sodium potassium
l-tartrate, 0.02 M sodium oxamate, 0.1 M bicine/Trizma base pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.57 52.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.535 α = 90 b = 90.152 β = 90 c = 104.409 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2019-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.980 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.399 58.854 99.61 0.999 15.8 12.6 143762 13.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.399 1.436 0.823 0.884 0.313 0.825 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.399 58.854 143762 7047 99.617 0.162 0.1608 0.1604 0.185 0.1846 21.037
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] 0.565 0.076 -0.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.744 r_dihedral_angle_4_deg 16.711 r_dihedral_angle_3_deg 11.026 r_dihedral_angle_1_deg 7.233 r_lrange_it 2.585 r_lrange_other 2.521 r_scangle_it 2.094 r_scangle_other 2.094 r_mcangle_it 1.867 r_mcangle_other 1.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.744 r_dihedral_angle_4_deg 16.711 r_dihedral_angle_3_deg 11.026 r_dihedral_angle_1_deg 7.233 r_lrange_it 2.585 r_lrange_other 2.521 r_scangle_it 2.094 r_scangle_other 2.094 r_mcangle_it 1.867 r_mcangle_other 1.867 r_scbond_it 1.656 r_scbond_other 1.656 r_mcbond_it 1.475 r_mcbond_other 1.474 r_angle_other_deg 1.365 r_angle_refined_deg 1.295 r_rigid_bond_restr 0.906 r_nbd_refined 0.19 r_nbd_other 0.189 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.102 r_symmetry_xyhbond_nbd_refined 0.089 r_symmetry_nbd_refined 0.08 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_bond_refined_d 0.005 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 4605 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms
Software Software Software Name Purpose xia2 data reduction PHASER phasing Coot model building REFMAC refinement