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First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase APOBEC3G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IR2 PDB ENTRY 3IR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES, pH 7.5, 10% PEG 4000, 0.1M Magnesium Chloride, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 46.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.08 α = 90 b = 67.764 β = 107.38 c = 64.472 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 IMAGE PLATE RIGAKU RAXIS IV 2010-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.04 61.53 96.5 0.061 13.6 5 26971
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.11 94.3 0.539 4.9
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 PDB ENTRY 3IR2 2.04 28.01 25587 1329 96.01 0.23064 0.22825 0.2325 0.27569 0.2812 RANDOM 49.441
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] 0.76 -0.71 -1.24 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.364 r_dihedral_angle_4_deg 22.505 r_dihedral_angle_3_deg 19.573 r_dihedral_angle_1_deg 6.13 r_angle_refined_deg 1.399 r_angle_other_deg 1.232 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.364 r_dihedral_angle_4_deg 22.505 r_dihedral_angle_3_deg 19.573 r_dihedral_angle_1_deg 6.13 r_angle_refined_deg 1.399 r_angle_other_deg 1.232 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.003 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_it r_mcbond_other r_mcangle_it r_scbond_it 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 2874 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction