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Crystal structure of the DNA preQ0 insertase DpdA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 mixing 2 ul sample containing 4.0 mg/ml protein (81.5 uM), 0.5 mM guanine, 50 mM Tris (pH 7.5), 100 mM NaCl and 1 mM DTT with 3 ul reservoir solution containing 10% (w/v) polyethylene glycol (PEG) 8000, 8% (v/v) ethylene glycol (EG), 100 mM HEPES (pH 7.5), 0.1 mM ZnCl2, 3 mM reduced glutathione (GSH) and 3 mM oxidized glutathione (GSSG)
Crystal Properties Matthews coefficient Solvent content 2.77 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.102 α = 90 b = 141.768 β = 90 c = 42.496 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 CCD MARMOSAIC 325 mm CCD 2017-06-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.28149, 0.98397, 1.28268 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.51 73.59 87.1 0.103 0.107 0.029 0.999 21.8 12.8 16179
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.51 2.65 50.4 0.964 1.025 0.341 0.92 8.8
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 MAD THROUGHOUT 2.51 54.78 15348 790 87.09 0.1322 0.1298 0.1427 0.1785 0.1848 RANDOM 55.874
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] -1.43 1.96 -0.52
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.532 r_dihedral_angle_2_deg 35.327 r_sphericity_bonded 30.176 r_dihedral_angle_4_deg 21.219 r_dihedral_angle_3_deg 19.215 r_dihedral_angle_1_deg 6.617 r_rigid_bond_restr 2.082 r_angle_refined_deg 1.078 r_angle_other_deg 0.847 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.532 r_dihedral_angle_2_deg 35.327 r_sphericity_bonded 30.176 r_dihedral_angle_4_deg 21.219 r_dihedral_angle_3_deg 19.215 r_dihedral_angle_1_deg 6.617 r_rigid_bond_restr 2.082 r_angle_refined_deg 1.078 r_angle_other_deg 0.847 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3367 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction SOLVE phasing