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Crystal structure of NFIA monomer bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other the NFIC monomer structure solved in this study
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 5% (v/v) (+/-)-2-methyl-2,4-pentanediol, 0.1 M HEPES (pH 7.5), and 10% (w/v) PEG 10000
Crystal Properties Matthews coefficient Solvent content 4.14 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.677 α = 90 b = 48.463 β = 92 c = 105.882 γ = 90
Symmetry Space Group P 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 2024-04-06 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) 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 2.6 48.46 95.3 0.987 7.6 4.2 25334
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 2.6 2.72 70.8 0.584 1.2
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 2.6 19.97 23465 1297 93.02 0.19591 0.19314 0.2029 0.24759 0.2483 RANDOM 40.653
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] 0.02 0.02 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.62 r_dihedral_angle_4_deg 20.843 r_dihedral_angle_3_deg 19.848 r_long_range_B_other 8.492 r_long_range_B_refined 8.49 r_dihedral_angle_1_deg 7.343 r_scangle_other 5.96 r_mcangle_it 4.404 r_mcangle_other 4.402 r_scbond_it 3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.62 r_dihedral_angle_4_deg 20.843 r_dihedral_angle_3_deg 19.848 r_long_range_B_other 8.492 r_long_range_B_refined 8.49 r_dihedral_angle_1_deg 7.343 r_scangle_other 5.96 r_mcangle_it 4.404 r_mcangle_other 4.402 r_scbond_it 3.68 r_scbond_other 3.68 r_mcbond_it 2.822 r_mcbond_other 2.821 r_angle_refined_deg 1.945 r_angle_other_deg 1.172 r_chiral_restr 0.117 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2616 Nucleic Acid Atoms 854 Solvent Atoms 103 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing