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Wild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (crystal form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KEG Stripped of water, Zn2+, Cl- and ssDNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 285 A3A (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 hexa phosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.323 α = 90 b = 57.197 β = 99.37 c = 91.422 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 2021-09-28 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 2.94 49.05 99 0.166 0.094 0.985 5.8 3.9 11619 42.3
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 2.94 3.12 97.1 0.583 0.338 0.918 2.2 3.9
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 5KEGf 2.94 48.35 11041 567 98.93 0.2542 0.2512 0.2629 0.3103 0.3188 RANDOM 54.095
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] 7.43 6.32 -5.56 -3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.431 r_dihedral_angle_4_deg 20.662 r_dihedral_angle_3_deg 17.638 r_dihedral_angle_1_deg 6.361 r_angle_refined_deg 1.78 r_angle_other_deg 1.4 r_chiral_restr 0.099 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.431 r_dihedral_angle_4_deg 20.662 r_dihedral_angle_3_deg 17.638 r_dihedral_angle_1_deg 6.361 r_angle_refined_deg 1.78 r_angle_other_deg 1.4 r_chiral_restr 0.099 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2892 Nucleic Acid Atoms 448 Solvent Atoms Heterogen Atoms 37
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