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Crystal structure of Human FN3K bound with TDI-017425-NX-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, HANGING DROP 6.1 291 0.2 M ammonium sulfate, 0.1 M tri-sodium citrate (pH 6.1), and 23% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.83 59.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.829 α = 90 b = 110.11 β = 92.772 c = 87.744 γ = 90
Symmetry Space Group C 1 2 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 S 9M 2024-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2.833 93.875 89.3 0.588 0.635 0.238 0.927 3.9 7 23487
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 2.833 3.129 48.2 1.887 2.031 0.749 0.463 7.3
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 2.833 93.875 23487 1115 57.635 0.253 0.25258 0.2507 0.2533 0.2909 0.2919 RANDOM 18.63
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] 1.716 0.07 -1.155 -0.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.364 r_dihedral_angle_6_deg 9.165 r_dihedral_angle_1_deg 5.601 r_dihedral_angle_2_deg 2.818 r_lrange_it 1.395 r_lrange_other 1.395 r_angle_refined_deg 0.717 r_mcangle_it 0.409 r_mcangle_other 0.409 r_angle_other_deg 0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.364 r_dihedral_angle_6_deg 9.165 r_dihedral_angle_1_deg 5.601 r_dihedral_angle_2_deg 2.818 r_lrange_it 1.395 r_lrange_other 1.395 r_angle_refined_deg 0.717 r_mcangle_it 0.409 r_mcangle_other 0.409 r_angle_other_deg 0.279 r_scangle_it 0.243 r_scangle_other 0.243 r_mcbond_it 0.217 r_mcbond_other 0.217 r_nbd_refined 0.181 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.162 r_symmetry_nbd_refined 0.143 r_nbd_other 0.127 r_scbond_it 0.124 r_scbond_other 0.124 r_xyhbond_nbd_refined 0.121 r_symmetry_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.034 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9365 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 178
Software Software Software Name Purpose DIALS data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building