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Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NYT PDB ENTRY 2NYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 288 0.1 M Tris-HCl pH 8.0, 20% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.79 α = 110.75 b = 66.91 β = 94.41 c = 75.64 γ = 108.83
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD mirrors 2012-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 2.75 50 98.2 0.063 13.5 2 22096 22560 2 2 63.3
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 2.75 2.85 98.1 0.22 31 2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2NYT 2.751 36.457 2 22096 21463 1099 95.97 0.1954 0.1934 0.1938 0.2326 0.2347 49.503
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] -0.14 -3.36 -1.29 -0.17 0.78 -1.5
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.333 f_angle_d 0.765 f_chiral_restr 0.052 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5569 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling Locally data collection