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Crystal structure of the PFV N224H mutant intasome bound to 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 69.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.67 α = 90 b = 160.67 β = 90 c = 123.05 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 38.968 98.1 0.096 10.2 5.1 44545 -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 99 0.01 1.025 1.6 5.2 6463
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 38.97 44428 2249 97.19 0.21 0.2092 0.208 0.2022 0.2313 0.2275 RANDOM 65.7775
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] 1.67 1.67 -3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.902 r_dihedral_angle_4_deg 17.867 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_1_deg 5.849 r_scangle_it 2.879 r_scbond_it 1.668 r_angle_refined_deg 1.493 r_mcangle_it 1.242 r_mcbond_it 0.647 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.902 r_dihedral_angle_4_deg 17.867 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_1_deg 5.849 r_scangle_it 2.879 r_scbond_it 1.668 r_angle_refined_deg 1.493 r_mcangle_it 1.242 r_mcbond_it 0.647 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4372 Nucleic Acid Atoms 732 Solvent Atoms 189 Heterogen Atoms 75
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection