POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4HCC
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6
    Temperature 293.0
    Details The crystals grew in 1.65-1.68 M ammonium sulfate, 6.5-6.8% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate pH 6.0, 5 mM phenol, then soaked in the solution consisted of precipitant solution and 20 mM zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 63.04 α = 90
    b = 108.69 β = 90
    c = 158.4 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 315r
    Collection Date 2012-03-02
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.97930
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.95
    Resolution(Low) 30
    Number Reflections(All) 23347
    Number Reflections(Observed) 23141
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.091
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 2.95
    Resolution(Low) 3.0
    Percent Possible(All) 99.6
    R Merge I(Observed) 0.436
    Redundancy 7.1
    Number Unique Reflections(All) 1145
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.96
    Resolution(Low) 30.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 23347
    Number of Reflections(Observed) 23099
    Number of Reflections(R-Free) 1188
    Percent Reflections(Observed) 98.49
    R-Factor(Observed) 0.188
    R-Work 0.1849
    R-Free 0.2448
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 62.8263
    Anisotropic B[1][1] 2.55
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.35
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.2
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.96
    Shell Resolution(Low) 3.035
    Number of Reflections(R-Free) 75
    Number of Reflections(R-Work) 1315
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.315
    Percent Reflections(Observed) 89.27
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.004
    r_chiral_restr 0.077
    r_dihedral_angle_4_deg 16.784
    r_dihedral_angle_3_deg 16.186
    r_dihedral_angle_2_deg 37.557
    r_dihedral_angle_1_deg 5.298
    r_angle_refined_deg 1.046
    r_bond_refined_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7538
    Nucleic Acid Atoms 414
    Heterogen Atoms 57
    Solvent Atoms 20
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.6.0117
    data reduction SCALEPACK