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X-RAY DIFFRACTION
Materials and Methods page
2YNQ
  •   Crystallization Hide
    Crystallization Experiments
    pH 7
    Details 3 M MALONATE PH7.0, 10 MM ZNCL2
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 132.89 α = 90
    b = 110.62 β = 103.34
    c = 97.41 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD (QUANTUM 315R)
    Type ADSC
    Details MIRRORS
    Collection Date 2010-07-28
     
    Diffraction Radiation
    Monochromator SILICON
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I02
    Wavelength 0.9795
    Site DIAMOND
    Beamline I02
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.4
    Resolution(Low) 29.46
    Number Reflections(Observed) 52114
    Percent Possible(Observed) 97.4
    R Merge I(Observed) 0.07
    B(Isotropic) From Wilson Plot 56.6
    Redundancy 4.6
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.53
    Percent Possible(All) 96.3
    R Merge I(Observed) 0.44
    Mean I Over Sigma(Observed) 3.0
    Redundancy 4.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.4
    Resolution(Low) 94.782
    Cut-off Sigma(F) 1.0
    Number of Reflections(Observed) 52094
    Number of Reflections(R-Free) 2642
    Percent Reflections(Observed) 97.145
    R-Factor(Observed) 0.188
    R-Work 0.1862
    R-Free 0.2215
     
    Temperature Factor Modeling
    Mean Isotropic B Value 60.064
    Anisotropic B[1][1] -0.188
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.366
    Anisotropic B[2][2] -0.335
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.108
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4
    Shell Resolution(Low) 2.462
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 3649
    R-Factor(R-Work) 0.294
    R-Factor(R-Free) 0.342
    Percent Reflections(Observed) 97.248
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.113
    r_scbond_it 1.842
    r_mcangle_it 1.134
    r_mcbond_it 0.565
    r_nbd_refined 0.211
    r_gen_planes_refined 0.004
    r_chiral_restr 0.083
    r_dihedral_angle_4_deg 17.626
    r_dihedral_angle_3_deg 16.875
    r_dihedral_angle_2_deg 39.311
    r_dihedral_angle_1_deg 4.768
    r_angle_refined_deg 1.202
    r_bond_refined_d 0.011
    r_nbtor_refined 0.305
    r_xyhbond_nbd_refined 0.158
    r_metal_ion_refined 0.119
    r_symmetry_vdw_refined 0.194
    r_symmetry_hbond_refined 0.186
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5000
    Nucleic Acid Atoms 0
    Heterogen Atoms 35
    Solvent Atoms 246
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building PHASER