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X-RAY DIFFRACTION
Materials and Methods page
3CQD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.3
    Temperature 293.0
    Details 0.1 M sodium acetate, 12% PEG 6000, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 42.82 α = 90
    b = 86.83 β = 90
    c = 171.31 γ = 90
     
    Space Group
    Space Group Name:    P 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 130 mm
    Details MIRRORS
    Collection Date 2006-03-30
     
    Diffraction Radiation
    Monochromator Silicon
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type LNLS BEAMLINE D03B-MX1
    Wavelength List 1.438
    Site LNLS
    Beamline D03B-MX1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.98
    Resolution(Low) 20
    Number Reflections(All) 46352
    Number Reflections(Observed) 43478
    Percent Possible(Observed) 93.8
    R Merge I(Observed) 0.075
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 1.98
    Resolution(Low) 2.09
    Percent Possible(All) 90.1
    R Merge I(Observed) 0.302
    Mean I Over Sigma(Observed) 4.3
    R-Sym I(Observed) 0.302
    Redundancy 5.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.98
    Resolution(Low) 14.94
    Number of Reflections(all) 42925
    Number of Reflections(Observed) 41174
    Number of Reflections(R-Free) 2190
    Percent Reflections(Observed) 95.92
    R-Factor(Observed) 0.18881
    R-Work 0.18637
    R-Free 0.23377
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model ISOTROPIC
    Mean Isotropic B Value 24.153
    Anisotropic B[1][1] -0.11
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.01
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.1
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.983
    Shell Resolution(Low) 2.034
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2534
    R-Factor(R-Work) 0.226
    R-Factor(R-Free) 0.268
    Percent Reflections(Observed) 81.64
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.746
    r_scbond_it 1.702
    r_mcangle_it 0.932
    r_mcbond_it 0.546
    r_nbd_refined 0.208
    r_gen_planes_refined 0.005
    r_chiral_restr 0.087
    r_dihedral_angle_4_deg 20.688
    r_dihedral_angle_3_deg 16.136
    r_dihedral_angle_2_deg 37.644
    r_dihedral_angle_1_deg 5.501
    r_angle_refined_deg 1.483
    r_bond_refined_d 0.011
    r_nbtor_refined 0.304
    r_xyhbond_nbd_refined 0.151
    r_metal_ion_refined 0.017
    r_symmetry_vdw_refined 0.209
    r_symmetry_hbond_refined 0.136
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4502
    Nucleic Acid Atoms 0
    Heterogen Atoms 128
    Solvent Atoms 463
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019