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Structure of APOBEC3A (E72A inactive mutant) in complex with TTC-hairpin DNA substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KEG Stripped of H2O, Zn2+, Cl-, ssDNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 285 A3A-E72A (50 mM MES pH 6.0, 100 mM NaCl, 1 mM TCEP, 0.2 mM EDTA) was mixed with oligonucleotides (10 mM Tris/HCl pH 7.9, 1 mM EDTA) at 0.85 mM and 1.7 mM respectively. Dilution was done with protein buffer. The mixture was added to crystallization liquid 1 to 1 and the mixture was pipetted on siliconized glass disks and sealed on top of a reservoir of crystallization liquid for hanging drop crystallization at 12 degrees Celsius. The crystallization liquid has the following composition: 100 mM Bicine at pH 6.6, 200 mM NaCl, 20 mM putrescine, 1 mM TCEP, 1 mM inositol hexaphosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.51 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.917 α = 90 b = 56.904 β = 103.57 c = 91.549 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 EIGER X 9M 1 vertical and 2 horizontal focussing mirrors 2021-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953739 Australian Synchrotron MX2
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 2.22 47.99 97.3 0.092 0.11 0.059 0.995 6.2 3.4 26243 51
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 2.22 2.29 97.9 1.535 1.826 0.979 0.332 0.6 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5KEG 2.22 47.99 24929 1309 97.2 0.2396 0.2376 0.2772 0.284 RANDOM 62.63
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] -1.59 1.65 1.02 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.704 r_dihedral_angle_4_deg 20.66 r_dihedral_angle_3_deg 16.256 r_dihedral_angle_1_deg 7.364 r_angle_refined_deg 1.87 r_angle_other_deg 1.319 r_chiral_restr 0.111 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.704 r_dihedral_angle_4_deg 20.66 r_dihedral_angle_3_deg 16.256 r_dihedral_angle_1_deg 7.364 r_angle_refined_deg 1.87 r_angle_other_deg 1.319 r_chiral_restr 0.111 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3026 Nucleic Acid Atoms 520 Solvent Atoms 16 Heterogen Atoms 81
Software Software Software Name Purpose JBluIce-EPICS data collection XDS data reduction Aimless data scaling pointless data scaling MOLREP phasing REFMAC refinement Coot model building