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Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI Compound2
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 3.92 68.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.5 α = 90 b = 159.5 β = 90 c = 123.11 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 AREA DETECTOR ADSC 2010-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 1
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 2.74 39.014 99.6 0.154 6.1 4.7 41952 -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) 2.74 2.89 99.9 0.862 0.862 1.6 4.7 6051
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 2.74 39.01 41643 2091 98.61 0.21 0.2053 0.2038 0.1997 0.2338 0.2304 RANDOM 57.4132
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] 1.17 1.17 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.492 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_3_deg 16.419 r_dihedral_angle_1_deg 6.093 r_scangle_it 2.818 r_scbond_it 1.641 r_angle_refined_deg 1.556 r_mcangle_it 1.292 r_mcbond_it 0.669 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.492 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_3_deg 16.419 r_dihedral_angle_1_deg 6.093 r_scangle_it 2.818 r_scbond_it 1.641 r_angle_refined_deg 1.556 r_mcangle_it 1.292 r_mcbond_it 0.669 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4370 Nucleic Acid Atoms 732 Solvent Atoms 217 Heterogen Atoms 73
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection