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Crystal structure of Ferritin 2 from Caenorhabditis elegans, FTN-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2-methyl-2,4-pentanediol, Bis-Tris, Ammonium acetate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.84 α = 90 b = 154.84 β = 90 c = 128.763 γ = 90
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 EIGER X 16M 2021-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.468 50 99.7 0.081 0.034 0.998 9.4 6.8 256649
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.49 0.625 0.262 0.847
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 FREE R-VALUE 5WPN 1.468 49.505 256647 13172 99.621 0.16 0.1593 0.1594 0.1764 0.1765 17.418
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] -0.496 -0.496 0.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.272 r_dihedral_angle_4_deg 20.921 r_dihedral_angle_3_deg 12.193 r_dihedral_angle_1_deg 5.098 r_lrange_it 5.002 r_lrange_other 4.582 r_scangle_it 2.069 r_scangle_other 2.069 r_angle_other_deg 1.395 r_scbond_it 1.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.272 r_dihedral_angle_4_deg 20.921 r_dihedral_angle_3_deg 12.193 r_dihedral_angle_1_deg 5.098 r_lrange_it 5.002 r_lrange_other 4.582 r_scangle_it 2.069 r_scangle_other 2.069 r_angle_other_deg 1.395 r_scbond_it 1.318 r_scbond_other 1.317 r_angle_refined_deg 1.197 r_mcangle_other 1.112 r_mcangle_it 1.111 r_mcbond_it 0.701 r_mcbond_other 0.691 r_symmetry_xyhbond_nbd_refined 0.21 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.187 r_nbd_other 0.182 r_nbtor_refined 0.167 r_symmetry_nbd_other 0.157 r_xyhbond_nbd_other 0.135 r_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.053 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8196 Nucleic Acid Atoms Solvent Atoms 1407 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing