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Crystal structure of Human FN3K bound with TDI-017058-FA-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9H479-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1 M HEPES (pH 7.0) and 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.79 67.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.5 α = 90 b = 113.5 β = 90 c = 166.02 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 6M 2024-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.99999 SPring-8 BL45XU
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 2.45 48.54 100 0.144 0.149 0.039 0.999 20.2 26.8 40564
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 2.45 2.55 100 1.764 1.829 0.484 0.76 2.3 27.3
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-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 2.45 48.54 40563 2044 99.953 0.189 0.18935 0.187 0.1935 0.2329 0.2322 RANDOM 52.477
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] -0.179 -0.179 0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.583 r_dihedral_angle_6_deg 14.173 r_lrange_other 10.313 r_lrange_it 10.305 r_dihedral_angle_2_deg 9.422 r_scangle_it 8.169 r_scangle_other 8.168 r_dihedral_angle_1_deg 7.05 r_mcangle_other 5.891 r_mcangle_it 5.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.583 r_dihedral_angle_6_deg 14.173 r_lrange_other 10.313 r_lrange_it 10.305 r_dihedral_angle_2_deg 9.422 r_scangle_it 8.169 r_scangle_other 8.168 r_dihedral_angle_1_deg 7.05 r_mcangle_other 5.891 r_mcangle_it 5.887 r_scbond_it 5.4 r_scbond_other 5.399 r_mcbond_it 3.974 r_mcbond_other 3.974 r_angle_refined_deg 1.473 r_angle_other_deg 0.52 r_symmetry_xyhbond_nbd_refined 0.376 r_nbd_refined 0.22 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.157 r_nbd_other 0.132 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4691 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 157
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building