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Crystal structure of the PFV S217Q mutant intasome in complex with magnesium and the INSTI MK2048
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 3.97 68.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.17 α = 90 b = 160.17 β = 90 c = 123.7 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 2010-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97630 Diamond I04
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 2.68 39.187 98.9 0.101 11.2 5.5 45020 -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) 2.68 2.82 98.9 0.894 0.894 1.6 5.5 6473
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 2.68 38.85 44899 2260 98.3 0.21 0.2074 0.2056 0.2029 0.2408 0.2379 RANDOM 62.2024
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] 0.45 0.45 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.706 r_dihedral_angle_3_deg 17.197 r_dihedral_angle_4_deg 14.133 r_dihedral_angle_1_deg 6.35 r_scangle_it 2.964 r_scbond_it 1.725 r_angle_refined_deg 1.579 r_mcangle_it 1.32 r_mcbond_it 0.684 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.706 r_dihedral_angle_3_deg 17.197 r_dihedral_angle_4_deg 14.133 r_dihedral_angle_1_deg 6.35 r_scangle_it 2.964 r_scbond_it 1.725 r_angle_refined_deg 1.579 r_mcangle_it 1.32 r_mcbond_it 0.684 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4345 Nucleic Acid Atoms 732 Solvent Atoms 198 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