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DNA substrate selection by APOBEC3G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IR2 3IR2, 1QZH experimental model PDB 1QZH 3IR2, 1QZH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 298 100 mM HEPES pH7, 200 mM LiCl, and 20% (w/v) Polyethylene glycol (PEG) 6000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.072 α = 90 b = 79.072 β = 90 c = 266.411 γ = 90
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 PILATUS 6M 2012-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 2.9 44.19 97.5 0.105 0.064 0.7 5.1 3.3 35772
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 0.856 0.539 1.1 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 (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 3IR2, 1QZH 2.9 44.19 32909 1737 96.21 0.23665 0.23394 0.2171 0.28692 0.2657 RANDOM 88.213
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] 65 65 -130
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.406 r_dihedral_angle_3_deg 17.126 r_dihedral_angle_4_deg 15.888 r_long_range_B_refined 15.645 r_mcangle_it 8.786 r_dihedral_angle_1_deg 6.608 r_mcbond_it 5.581 r_scbond_it 5.545 r_angle_refined_deg 1.942 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.406 r_dihedral_angle_3_deg 17.126 r_dihedral_angle_4_deg 15.888 r_long_range_B_refined 15.645 r_mcangle_it 8.786 r_dihedral_angle_1_deg 6.608 r_mcbond_it 5.581 r_scbond_it 5.545 r_angle_refined_deg 1.942 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11169 Nucleic Acid Atoms 577 Solvent Atoms 57 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing