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Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 10% (W/V) PEG 2K, 200 MM KCL, 50 MM NA CACODYLATE (PH=6) 2 MM GDCL3,
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.86 α = 90 b = 135.7 β = 90 c = 51.46 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M TOROIDAL MIRROR 2013-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 97.2 0.07 12 2.8 143744 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.65 96.7 0.82 1.9 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 SAD THROUGHOUT NONE 1.6 50.01 72884 3895 99.2 0.15818 0.1569 0.1716 0.18245 0.1953 RANDOM 25.586
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] 1.79 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_3_deg 13.495 r_dihedral_angle_4_deg 6.185 r_dihedral_angle_1_deg 5.848 r_scbond_it 4.039 r_mcangle_it 2.88 r_angle_refined_deg 2.473 r_mcbond_it 1.993 r_mcbond_other 1.975 r_angle_other_deg 1.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_3_deg 13.495 r_dihedral_angle_4_deg 6.185 r_dihedral_angle_1_deg 5.848 r_scbond_it 4.039 r_mcangle_it 2.88 r_angle_refined_deg 2.473 r_mcbond_it 1.993 r_mcbond_other 1.975 r_angle_other_deg 1.705 r_chiral_restr 0.151 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_bond_other_d 0.011 r_gen_planes_other 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3909 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELX phasing SHARP phasing BUCCANEER phasing