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Structure of the N-terminal didomain d1_d2 of the Thrombospondin type-1 domain-containing 7A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M sodium chloride, 0.1 M bis-tris, 1.5 M ammonium sulphate, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.99 58.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.843 α = 90 b = 108.714 β = 90 c = 53.536 γ = 90
Symmetry Space Group C 2 2 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 X CdTe 16M 2020-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.3 57.56 99.8 1 10.8 13.2 9135
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.62 1
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 2.3 57.555 9111 475 99.792 0.23 0.227 0.2272 0.2916 0.2918 58.873
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] 1.122 -2.418 1.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.893 r_dihedral_angle_6_deg 13.799 r_lrange_other 13.438 r_lrange_it 13.43 r_scangle_it 11.161 r_scangle_other 11.154 r_mcangle_other 8.522 r_mcangle_it 8.495 r_dihedral_angle_1_deg 7.411 r_dihedral_angle_2_deg 7.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.893 r_dihedral_angle_6_deg 13.799 r_lrange_other 13.438 r_lrange_it 13.43 r_scangle_it 11.161 r_scangle_other 11.154 r_mcangle_other 8.522 r_mcangle_it 8.495 r_dihedral_angle_1_deg 7.411 r_dihedral_angle_2_deg 7.249 r_scbond_it 7.237 r_scbond_other 7.231 r_mcbond_it 5.639 r_mcbond_other 5.622 r_angle_refined_deg 1.6 r_angle_other_deg 0.507 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.186 r_nbd_other 0.135 r_symmetry_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.103 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1022 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing