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Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 17% PEG 4000, 0.02 M NaI, 0.6 M Ammonium sulfate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.251 α = 90 b = 115.304 β = 106.64 c = 101.082 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2021-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.51 44.65 97.8 0.0074 0.99 10.71 3.77 200406
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.61 94.7 0.228 0.26
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 SAD THROUGHOUT 1.51 44.65 198247 2105 97.84 0.15423 0.15389 0.1653 0.18632 0.1937 RANDOM 30.94
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] 9.16 -3.84 -9.31 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.22 r_dihedral_angle_4_deg 12.722 r_dihedral_angle_3_deg 11.498 r_dihedral_angle_1_deg 6.585 r_long_range_B_refined 5.028 r_long_range_B_other 5.028 r_scangle_other 2.839 r_mcangle_it 2.389 r_mcangle_other 2.389 r_scbond_it 2.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.22 r_dihedral_angle_4_deg 12.722 r_dihedral_angle_3_deg 11.498 r_dihedral_angle_1_deg 6.585 r_long_range_B_refined 5.028 r_long_range_B_other 5.028 r_scangle_other 2.839 r_mcangle_it 2.389 r_mcangle_other 2.389 r_scbond_it 2.263 r_scbond_other 2.26 r_mcbond_it 1.931 r_mcbond_other 1.918 r_angle_refined_deg 1.297 r_angle_other_deg 1.258 r_rigid_bond_restr 1.015 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6576 Nucleic Acid Atoms Solvent Atoms 1224 Heterogen Atoms 294
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction HKL2Map phasing