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Structure of Nfox from the gut microbiome of Hermetia illucens
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.1 M SPG buffer pH9.0, 25 % w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.9 α = 90 b = 75.9 β = 90 c = 138.82 γ = 120
Symmetry Space Group P 32 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 EIGER X 16M 2025-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979183 SSRF BL10U2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.6 26.81 100 0.99 17 18.5 61850
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.788 2.3
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 (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 1.6 26.81 58597 3197 99.96 0.17172 0.17075 0.1838 0.18993 0.2008 RANDOM 22.223
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] 0.29 0.15 0.29 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.04 r_dihedral_angle_1_deg 6.841 r_long_range_B_refined 5.538 r_long_range_B_other 5.517 r_dihedral_angle_2_deg 5.13 r_scangle_other 4.988 r_scbond_other 3.325 r_scbond_it 3.322 r_mcangle_it 2.805 r_mcangle_other 2.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.04 r_dihedral_angle_1_deg 6.841 r_long_range_B_refined 5.538 r_long_range_B_other 5.517 r_dihedral_angle_2_deg 5.13 r_scangle_other 4.988 r_scbond_other 3.325 r_scbond_it 3.322 r_mcangle_it 2.805 r_mcangle_other 2.805 r_mcbond_it 2.019 r_mcbond_other 2.006 r_angle_refined_deg 1.938 r_angle_other_deg 0.652 r_chiral_restr 0.101 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3077 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PHENIX phasing PDB_EXTRACT data extraction