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Crystal structure of Human FN3K bound with TDI-016948-NX-2
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 8 291 1.5 M ammonium sulfate, 0.1 M sodium citrate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.78 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.918 α = 90 b = 110.918 β = 90 c = 127.401 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 EIGER2 S 9M 2024-01-13 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 2.238 83.66 99.1 0.251 0.265 0.102 0.994 14.1 13.8 36766
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 2.238 2.31 90.2 1.576 1.71 0.656 0.756 13.3
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 2.239 83.655 36745 1831 99.043 0.201 0.2005 0.1979 0.2043 0.252 0.2581 RANDOM 47.761
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] 1.292 1.292 -2.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.225 r_dihedral_angle_6_deg 14.344 r_dihedral_angle_3_deg 14.179 r_lrange_it 7.436 r_lrange_other 7.366 r_dihedral_angle_1_deg 6.809 r_scangle_it 4.597 r_scangle_other 4.587 r_mcangle_it 4.282 r_mcangle_other 4.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.225 r_dihedral_angle_6_deg 14.344 r_dihedral_angle_3_deg 14.179 r_lrange_it 7.436 r_lrange_other 7.366 r_dihedral_angle_1_deg 6.809 r_scangle_it 4.597 r_scangle_other 4.587 r_mcangle_it 4.282 r_mcangle_other 4.281 r_scbond_it 2.743 r_scbond_other 2.731 r_mcbond_it 2.639 r_mcbond_other 2.639 r_angle_refined_deg 0.977 r_angle_other_deg 0.351 r_nbd_refined 0.212 r_nbd_other 0.2 r_symmetry_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.178 r_symmetry_nbd_refined 0.174 r_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 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 4329 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 105
Software Software Software Name Purpose XDS data reduction autoPROC data processing Aimless data scaling PHASER phasing REFMAC refinement Coot model building