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Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI PICA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OYB PDB entry 3OYB
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 68.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.96 α = 90 b = 159.96 β = 90 c = 123.77 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 MARMOSAIC 225 mm CCD 2010-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00000 SLS X06DA
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 2.66 38.796 99.6 0.077 10.4 3.7 46307 -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) 2.66 2.8 100 0.613 0.613 2 3.7 6693
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-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 3OYB 2.66 38.8 46168 2333 99.11 0.21 0.2032 0.2019 0.1969 0.2261 0.222 RANDOM 56.4308
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] 1.23 1.23 -2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.831 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_3_deg 16.419 r_dihedral_angle_1_deg 5.978 r_scangle_it 2.814 r_scbond_it 1.646 r_angle_refined_deg 1.478 r_mcangle_it 1.312 r_mcbond_it 0.681 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.831 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_3_deg 16.419 r_dihedral_angle_1_deg 5.978 r_scangle_it 2.814 r_scbond_it 1.646 r_angle_refined_deg 1.478 r_mcangle_it 1.312 r_mcbond_it 0.681 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4367 Nucleic Acid Atoms 732 Solvent Atoms 245 Heterogen Atoms 63
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection PHASER phasing