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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4G4G
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 289.0
    Details 30% PEG 3350, 0.1M Tris(hydroxymethyl)aminomethane hydrochloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 45.97 α = 90
    b = 58.74 β = 90
    c = 136.16 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 MAR CCD 165 mm
    Details mirrors
    Collection Date 2010-11-23
     
    Diffraction Radiation
    Monochromator Si (111) horizontally focussing
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type EMBL/DESY, HAMBURG BEAMLINE X13
    Wavelength List 0.8123
    Site EMBL/DESY, HAMBURG
    Beamline X13
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.55
    Resolution(Low) 19.45
    Number Reflections(All) 51271
    Number Reflections(Observed) 51271
    Percent Possible(Observed) 94.5
    R Merge I(Observed) 0.069
    B(Isotropic) From Wilson Plot 13.5
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 1.55
    Resolution(Low) 1.63
    Percent Possible(All) 95.9
    R Merge I(Observed) 0.498
    Mean I Over Sigma(Observed) 2.5
    Redundancy 3.5
    Number Unique Reflections(All) 7498
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.55
    Resolution(Low) 19.36
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 48582
    Number of Reflections(Observed) 48582
    Number of Reflections(R-Free) 2610
    Percent Reflections(Observed) 94.05
    R-Factor(All) 0.20639
    R-Factor(Observed) 0.20639
    R-Work 0.20385
    R-Free 0.25371
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 17.129
    Anisotropic B[1][1] -0.01
    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] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.55
    Shell Resolution(Low) 1.59
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3377
    R-Factor(R-Work) 0.247
    R-Factor(R-Free) 0.333
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 6.255
    r_sphericity_free 23.768
    r_rigid_bond_restr 1.436
    r_gen_planes_refined 0.003
    r_chiral_restr 0.066
    r_dihedral_angle_4_deg 16.193
    r_dihedral_angle_3_deg 12.741
    r_dihedral_angle_2_deg 28.488
    r_dihedral_angle_1_deg 4.956
    r_angle_refined_deg 0.967
    r_bond_refined_d 0.005
     
    Coordinate Error
    Luzzati ESD(Observed) 0.2138
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2722
    Nucleic Acid Atoms 0
    Heterogen Atoms 68
    Solvent Atoms 412
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building PHASER
    data collection DNA