☰ Navigation Tabs
Structure of Thermocrinis minervae double ferritin-like protein (ThmDFLP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A1M6SI41-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 40% v/v Ethanol, 5% w/v PEG 1000, 0.1 M Phosphate/citrate buffer, pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.08 40.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.955 α = 90 b = 105.16 β = 90.273 c = 89.144 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 X 16M 2024-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.97918 SSRF BL17UM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.453 46.503 65.1 0.345 0.374 0.142 0.982 5.1 6.9 28140
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) 2.453 2.716 1.595 1.72 0.638 0.598 1.4 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT AF-A0A1M6SI41-F1 2.466 46.546 27917 1321 65.542 0.246 0.2433 0.2435 0.2931 0.29 39.953
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] -0.745 0.762 0.935 -0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.374 r_lrange_it 10.864 r_lrange_other 10.864 r_dihedral_angle_6_deg 9.429 r_scangle_it 7.81 r_scangle_other 7.809 r_mcangle_it 5.48 r_mcangle_other 5.479 r_scbond_it 4.705 r_scbond_other 4.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.374 r_lrange_it 10.864 r_lrange_other 10.864 r_dihedral_angle_6_deg 9.429 r_scangle_it 7.81 r_scangle_other 7.809 r_mcangle_it 5.48 r_mcangle_other 5.479 r_scbond_it 4.705 r_scbond_other 4.705 r_dihedral_angle_2_deg 4.035 r_dihedral_angle_1_deg 3.757 r_mcbond_it 3.433 r_mcbond_other 3.433 r_angle_refined_deg 0.546 r_symmetry_xyhbond_nbd_refined 0.388 r_symmetry_nbd_refined 0.334 r_nbd_other 0.331 r_xyhbond_nbd_refined 0.248 r_nbd_refined 0.237 r_symmetry_nbd_other 0.22 r_angle_other_deg 0.19 r_nbtor_refined 0.186 r_metal_ion_refined 0.129 r_symmetry_xyhbond_nbd_other 0.098 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.025 r_bond_refined_d 0.001 r_gen_planes_refined 0.001 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9143 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction STARANISO data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction