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Crystal structure of the Prototype Foamy Virus (PFV) N224H mutant intasome in complex with magnesium and Dolutegravir (S/GSK1349572)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.96 68.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.44 α = 90 b = 160.44 β = 90 c = 123.03 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315 2010-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97630 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.55 39.141 99.2 0.086 2 8.6 52365 52365 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.69 95.5 0.955 0.955 0.8 6.7 7217
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3OYN 2.55 39.14 52761 52270 2639 99.07 0.21 0.2095 0.2084 0.2014 0.2301 0.2229 RANDOM 59.3555
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] 1.13 1.13 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.276 r_dihedral_angle_4_deg 16.362 r_dihedral_angle_3_deg 16.328 r_dihedral_angle_1_deg 6.12 r_scangle_it 3.085 r_scbond_it 1.819 r_angle_refined_deg 1.524 r_mcangle_it 1.386 r_mcbond_it 0.715 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.276 r_dihedral_angle_4_deg 16.362 r_dihedral_angle_3_deg 16.328 r_dihedral_angle_1_deg 6.12 r_scangle_it 3.085 r_scbond_it 1.819 r_angle_refined_deg 1.524 r_mcangle_it 1.386 r_mcbond_it 0.715 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4378 Nucleic Acid Atoms 732 Solvent Atoms 199 Heterogen Atoms 81
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection PHASER phasing