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X-RAY DIFFRACTION
Materials and Methods page
1Q84
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.75
    Temperature 277.0
    Details 25-32% PEG 600, 20-100 mM Hepes, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 79.27 α = 90
    b = 111.76 β = 90
    c = 227.17 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2002-12-05
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength List 0.933
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.45
    Resolution(Low) 20
    Number Reflections(Observed) 74834
    Percent Possible(Observed) 99.8
    B(Isotropic) From Wilson Plot 57.0
    Redundancy 3.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.45
    Resolution(Low) 20.0
    Number of Reflections(Observed) 73140
    Number of Reflections(R-Free) 1507
    Percent Reflections(Observed) 99.69
    R-Factor(Observed) 0.18487
    R-Work 0.18427
    R-Free 0.21404
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 38.036
    Anisotropic B[1][1] 3.32
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.04
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -6.36
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.45
    Shell Resolution(Low) 2.513
    Number of Reflections(R-Free) 102
    Number of Reflections(R-Work) 5256
    R-Factor(R-Work) 0.264
    R-Factor(R-Free) 0.27
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_nbtor_other 0.086
    r_nbd_other 0.234
    r_nbd_refined 0.201
    r_gen_planes_other 0.003
    r_gen_planes_refined 0.006
    r_chiral_restr 0.085
    r_dihedral_angle_1_deg 6.421
    r_angle_other_deg 1.1
    r_angle_refined_deg 1.5
    r_bond_other_d 0.002
    r_bond_refined_d 0.015
    r_xyhbond_nbd_refined 0.163
    r_symmetry_vdw_refined 0.123
    r_symmetry_vdw_other 0.363
    r_symmetry_hbond_refined 0.209
    r_mcbond_it 0.633
    r_mcangle_it 1.259
    r_scbond_it 2.003
    r_scangle_it 3.451
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8314
    Nucleic Acid Atoms 0
    Heterogen Atoms 147
    Solvent Atoms 338
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution CNS
    Structure Refinement REFMAC 5.1.24
     
    Software
    refinement REFMAC version: 5.1.24