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APOBEC3A E72A inactive mutant in complex with ATTC-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 hex phosphate (phytic acid) and 45 % pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.001 α = 90 b = 57.229 β = 106.478 c = 92.752 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 1.91 48.173 98.4 0.09 0.057 0.996 7.5 3.4 42309 26.3
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 1.91 1.96 94.2 0.913 0.589 0.471 1 3.3
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 1.912 48.173 42293 2103 98.37 0.202 0.2001 0.2072 0.2317 0.2395 RANDOM 34.801
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] 1.559 0.376 -0.657 -0.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.709 r_dihedral_angle_4_deg 20.832 r_dihedral_angle_3_deg 14.828 r_lrange_it 7.399 r_lrange_other 7.399 r_dihedral_angle_1_deg 6.715 r_scangle_it 5.504 r_scangle_other 5.498 r_mcangle_it 3.962 r_mcangle_other 3.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.709 r_dihedral_angle_4_deg 20.832 r_dihedral_angle_3_deg 14.828 r_lrange_it 7.399 r_lrange_other 7.399 r_dihedral_angle_1_deg 6.715 r_scangle_it 5.504 r_scangle_other 5.498 r_mcangle_it 3.962 r_mcangle_other 3.962 r_scbond_it 3.409 r_scbond_other 3.399 r_mcbond_it 2.538 r_mcbond_other 2.537 r_angle_refined_deg 1.737 r_angle_other_deg 1.385 r_symmetry_nbd_refined 0.231 r_symmetry_nbd_other 0.215 r_nbd_refined 0.214 r_nbd_other 0.211 r_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.176 r_ncsr_local_group_2 0.145 r_chiral_restr 0.107 r_symmetry_xyhbond_nbd_other 0.105 r_ncsr_local_group_1 0.102 r_metal_ion_refined 0.095 r_symmetry_nbtor_other 0.083 r_gen_planes_refined 0.013 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3031 Nucleic Acid Atoms 614 Solvent Atoms 157 Heterogen Atoms 55
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