POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2YMO
  •   Crystallization Hide
    Crystallization Experiments
    Details 20 MM CALCIUM CHLORIDE DIHYDRATE, 20 MM CADMIUM CHLORIDE HYDRATE, 20 MM COBALT CHLORIDE HEXAHYDRATE AND 20% PEG 3350
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 41.66 α = 90
    b = 76.87 β = 90
    c = 85.05 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 (MX-325)
    Type MARRESEARCH
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-2
    Wavelength 0.9795
    Site SSRL
    Beamline BL9-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.9
    Resolution(Low) 42.52
    Number Reflections(Observed) 22181
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.06
    Redundancy 7.2
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 2.0
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.51
    Mean I Over Sigma(Observed) 3.8
    Redundancy 7.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 42.5
    Number of Reflections(Observed) 21005
    Number of Reflections(R-Free) 1129
    Percent Reflections(Observed) 99.66
    R-Factor(Observed) 0.2424
    R-Work 0.24015
    R-Free 0.28848
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 41.092
    Anisotropic B[1][1] -1.64
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.24
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.61
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.949
    Number of Reflections(R-Free) 73
    Number of Reflections(R-Work) 1533
    R-Factor(R-Work) 0.306
    R-Factor(R-Free) 0.391
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.013
    r_chiral_restr 0.108
    r_dihedral_angle_4_deg 26.907
    r_dihedral_angle_3_deg 20.624
    r_dihedral_angle_2_deg 41.342
    r_dihedral_angle_1_deg 7.819
    r_angle_refined_deg 1.295
    r_bond_refined_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1760
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 51
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) IMOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0029
     
    Software
    refinement REFMAC version: 5.7.0029
    model building PHASER