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Zinc-free APOBEC3A (inactive E72A mutant) in complex with TTC-hairpin DNA substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KEG
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 2.6 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.75 α = 90 b = 57.352 β = 105.78 c = 93.739 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 16M 1 vertical and 2 horizontal focussing mirrors 2022-09-28 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) 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 2.01 48.4 97.8 0.113 0.081 0.992 6.1 2.8 36510 38.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.15 88.3 1.294 0.955 0.188 0.7 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 MOLECULAR REPLACEMENT THROUGHOUT 5KEG 2.01 40.94 34669 1827 97.58 0.23292 0.23118 0.2333 0.26586 0.2689 RANDOM 43.944
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] 2.5 1.66 -2.78 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.951 r_dihedral_angle_4_deg 22.543 r_dihedral_angle_3_deg 15.109 r_long_range_B_refined 7.493 r_long_range_B_other 7.483 r_dihedral_angle_1_deg 7.017 r_scangle_other 5.13 r_mcangle_it 3.813 r_mcangle_other 3.813 r_scbond_it 3.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.951 r_dihedral_angle_4_deg 22.543 r_dihedral_angle_3_deg 15.109 r_long_range_B_refined 7.493 r_long_range_B_other 7.483 r_dihedral_angle_1_deg 7.017 r_scangle_other 5.13 r_mcangle_it 3.813 r_mcangle_other 3.813 r_scbond_it 3.178 r_scbond_other 3.178 r_mcbond_it 2.389 r_mcbond_other 2.389 r_angle_refined_deg 1.976 r_angle_other_deg 1.357 r_chiral_restr 0.116 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2992 Nucleic Acid Atoms 520 Solvent Atoms 81 Heterogen Atoms 74
Software Software Software Name Purpose XDS data reduction JBluIce-EPICS data collection Aimless data scaling pointless data scaling MOLREP phasing REFMAC refinement Coot model building