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Crystal Structure of human exonuclease 1 (Exo1) with DNA and compound 20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% PEG 3350, 0.2 M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.37 48.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.836 α = 90 b = 69.836 β = 90 c = 181.661 γ = 90
Symmetry Space Group P 43 21 2
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 2020-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
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 1.898 65.19 95.2 0.999 21.2 25.7 24543
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 1.898 2.081 0.643
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 1.9 65.19 24541 1979 67.4 0.2392 0.236 0.2255 0.2745 0.264 RANDOM 57.92
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] 1.9316 1.9316 -3.8632
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.87 t_omega_torsion 3.02 t_angle_deg 1.35 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_utility_distance
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.87 t_omega_torsion 3.02 t_angle_deg 1.35 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2729 Nucleic Acid Atoms 426 Solvent Atoms 88 Heterogen Atoms 38
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling PHASER phasing