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Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI MK2048
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OY9 PDB entry 3OY9
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 3.95 68.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.93 α = 90 b = 159.93 β = 90 c = 123.33 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 2.54 39.105 99.5 0.104 11.6 5.4 52789 -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) 2.54 2.68 99.6 0.01 1.044 1.6 5.4 7596
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 3OY9 2.54 39.1 52679 2668 99.08 0.21 0.2046 0.2035 0.1977 0.2239 0.22 RANDOM 53.5305
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] 1.27 1.27 -2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.814 r_dihedral_angle_4_deg 17.824 r_dihedral_angle_3_deg 15.631 r_dihedral_angle_1_deg 6.082 r_scangle_it 3.08 r_scbond_it 1.831 r_angle_refined_deg 1.507 r_mcangle_it 1.404 r_mcbond_it 0.727 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.814 r_dihedral_angle_4_deg 17.824 r_dihedral_angle_3_deg 15.631 r_dihedral_angle_1_deg 6.082 r_scangle_it 3.08 r_scbond_it 1.831 r_angle_refined_deg 1.507 r_mcangle_it 1.404 r_mcbond_it 0.727 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4343 Nucleic Acid Atoms 732 Solvent Atoms 252 Heterogen Atoms 71
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection