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The crystal structure of FAN1 Nuclease bound to 5' phosphorylated p(dG)/3'(dT-dT-dT-dT) double flap DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Hepes/MOPS pH: 7.25, 0.1M Sodium formate 0.1M Ammonium acetate 0.1M Sodium citrate tribasic dihydrate 0.1M Potassium sodium tartrate tetrahydrate 0.1M Sodium oxamate
21% v/v Ethylene glycol 21 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.01 59.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.626 α = 90 b = 100.547 β = 90 c = 112.879 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2023-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9537 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.645 43.395 99.9 0.071 0.999 16.6 11.2 31091
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 2.645 2.691 0.845
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.645 43.395 31090 823 99.849 0.235 0.2343 0.2357 0.2731 0.2665 84.729
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] -6.12 8.218 -2.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.263 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_3_deg 13.919 r_lrange_it 7.983 r_lrange_other 7.981 r_dihedral_angle_1_deg 6.179 r_mcangle_it 5.821 r_mcangle_other 5.82 r_scangle_it 5.435 r_scangle_other 5.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.263 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_3_deg 13.919 r_lrange_it 7.983 r_lrange_other 7.981 r_dihedral_angle_1_deg 6.179 r_mcangle_it 5.821 r_mcangle_other 5.82 r_scangle_it 5.435 r_scangle_other 5.435 r_mcbond_it 3.767 r_mcbond_other 3.757 r_scbond_it 3.447 r_scbond_other 3.447 r_angle_refined_deg 1.249 r_angle_other_deg 1.179 r_nbd_other 0.161 r_nbd_refined 0.159 r_nbtor_refined 0.159 r_symmetry_nbd_other 0.151 r_xyhbond_nbd_refined 0.107 r_symmetry_xyhbond_nbd_refined 0.083 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.055 r_symmetry_nbd_refined 0.031 r_xyhbond_nbd_other 0.02 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_symmetry_xyhbond_nbd_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4785 Nucleic Acid Atoms 816 Solvent Atoms 16 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing