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Wild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (crystal form 2)
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 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 2.3 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.943 α = 90 b = 56.365 β = 104.985 c = 90.113 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 2021-09-23 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 2.799 48.291 97.8 0.183 0.118 0.979 4.5 3.3 11861 57
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 2.8 2.95 92.8 1.157 0.735 0.466 0.8 3.4
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 (All) 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 2.799 48.291 11852 623 97.724 0.261 0.2577 0.2616 0.3182 0.3189 RANDOM 60.975
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] 4.278 1.154 -2.679 -1.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 23.042 r_dihedral_angle_3_deg 15.86 r_lrange_it 10.495 r_lrange_other 10.44 r_dihedral_angle_1_deg 7.144 r_scangle_it 5.221 r_scangle_other 5.169 r_mcangle_it 5.097 r_mcangle_other 5.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 23.042 r_dihedral_angle_3_deg 15.86 r_lrange_it 10.495 r_lrange_other 10.44 r_dihedral_angle_1_deg 7.144 r_scangle_it 5.221 r_scangle_other 5.169 r_mcangle_it 5.097 r_mcangle_other 5.096 r_scbond_it 3.131 r_mcbond_it 3.098 r_mcbond_other 3.085 r_scbond_other 3.056 r_angle_refined_deg 1.64 r_angle_other_deg 1.352 r_nbd_other 0.288 r_symmetry_nbd_other 0.236 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_other 0.215 r_symmetry_nbd_refined 0.215 r_xyhbond_nbd_refined 0.213 r_nbtor_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.101 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.087 r_metal_ion_refined 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2924 Nucleic Acid Atoms 404 Solvent Atoms 2 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction JBluIce-EPICS data collection Aimless data scaling pointless data scaling MOLREP phasing Coot model building