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X-RAY DIFFRACTION
Materials and Methods page
2XWY
  •   Crystallization Hide
    Crystallization Experiments
    pH 6
    Details SOAKING WITH COMPOUND MK3281 WAS PERFORMED AT 4 DEG C BY TRANSFERRING THE APO-NS5B CRYSTALS FOR 10 MIN IN A SOLUTION CONTAINING 100 MM 2-MORPHOLINOETHANESULFONIC ACID (MES), PH 6.0, 14% POLYETHYLENE GLYCOL (PEG) 8,000, 14% 2- PROPANOL, 2.5 MM TCEP, 10 MM MNCL2 AND 2.5 MM OF COMPOUND MK3281. THE CRYSTALS WERE THEN TRANSFERRED FOR 1 MIN TO A CRYO-PROTECTANT SOLUTION CONTAINING 100 MM MES PH 6.0, 14% POLYETHYLENE GLYCOL PEG 8,000, 14% 2-PROPANOL, 18% 2-METHYL-2,5 PENTANEDIOL (MPD), 2.5 MM TCEP, 5 MM MNCL2 AND 1.25 MM COMPOUND MK3281 AND THEN PLUNGED DIRECTLY INTO LIQUID NITROGEN.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 66.98 α = 90
    b = 94.27 β = 90
    c = 95.14 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD (QUANTUM 210)
    Type ADSC
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-1
    Wavelength 1.033
    Site ESRF
    Beamline ID14-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.53
    Resolution(Low) 20
    Number Reflections(Observed) 20692
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.09
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 2.53
    Resolution(Low) 2.67
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.53
    Mean I Over Sigma(Observed) 1.5
    Redundancy 3.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.53
    Resolution(Low) 95.35
    Number of Reflections(Observed) 19605
    Number of Reflections(R-Free) 1056
    Percent Reflections(Observed) 99.63
    R-Factor(Observed) 0.23727
    R-Work 0.23332
    R-Free 0.31016
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 54.851
    Anisotropic B[1][1] 1.15
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -5.32
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.17
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.53
    Shell Resolution(Low) 2.596
    Number of Reflections(R-Free) 70
    Number of Reflections(R-Work) 1384
    R-Factor(R-Work) 0.346
    R-Factor(R-Free) 0.412
    Percent Reflections(Observed) 97.39
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.504
    r_scbond_it 1.543
    r_mcangle_it 0.916
    r_mcbond_it 0.468
    r_gen_planes_refined 0.006
    r_chiral_restr 0.085
    r_dihedral_angle_4_deg 17.26
    r_dihedral_angle_3_deg 18.535
    r_dihedral_angle_2_deg 33.962
    r_dihedral_angle_1_deg 5.734
    r_angle_refined_deg 1.349
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3911
    Nucleic Acid Atoms 0
    Heterogen Atoms 37
    Solvent Atoms 130
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution AMORE
    Structure Refinement REFMAC 5.5.0102
     
    Software
    refinement REFMAC version: 5.5.0102
    model building AMORE