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Crystal structure of the DNA preQ0 insertase DpdA bound to preQ0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.25 293.15 Large single crystals were grown at 20C in sitting drops by mixing 2 ul of sample containing 8 mg/ml protein, 0.9 mM preQ0, 30 mM KCl, 20 mM Tris (pH 7.5) and 2 mM TCEP-HCl with 2 ul of crystallization solution containing 12 percent (w/v) polyethylene glycol 3,350 and 100 mM Bis-Tris (pH 6.25). Crystals were cryoprotected by quick dipping in a drop of crystallization solution supplemented with 35 percent (v/v) glycerol, followed by flash cooling in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.64 53.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.245 α = 90 b = 141.087 β = 90 c = 42.424 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 PILATUS3 2M 2023-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00003 ALS 8.2.2
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 1.66 47.03 100 0.079 0.086 0.034 0.999 12.9 6.4 62189
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 1.66 1.69 99.9 1.882 2.104 0.925 0.33 5
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 1.66 43.16 59036 3087 99.9 0.179 0.177 0.1903 0.208 0.2179 RANDOM 30.16
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] -0.35 0.08 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.799 r_long_range_B_refined 6.8 r_long_range_B_other 6.701 r_dihedral_angle_2_deg 6.501 r_dihedral_angle_1_deg 5.377 r_scangle_other 3.837 r_mcangle_it 2.663 r_mcangle_other 2.662 r_scbond_it 2.324 r_scbond_other 2.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.799 r_long_range_B_refined 6.8 r_long_range_B_other 6.701 r_dihedral_angle_2_deg 6.501 r_dihedral_angle_1_deg 5.377 r_scangle_other 3.837 r_mcangle_it 2.663 r_mcangle_other 2.662 r_scbond_it 2.324 r_scbond_other 2.324 r_mcbond_it 1.624 r_mcbond_other 1.623 r_angle_refined_deg 1.379 r_angle_other_deg 0.513 r_chiral_restr 0.071 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3376 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction