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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YPJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 277.0
    Details phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.52 α = 90
    b = 71.81 β = 99.87
    c = 71.31 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 IMAGE PLATE
    Type RIGAKU RAXIS IV
    Details Osmic mirrors
    Collection Date 2005-01-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RU300
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.78
    Resolution(Low) 50
    Number Reflections(Observed) 32153
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.076
    Redundancy 1.5
     
    High Resolution Shell Details
    Resolution(High) 1.78
    Resolution(Low) 1.81
    Percent Possible(All) 98.0
    R Merge I(Observed) 0.332
    Mean I Over Sigma(Observed) 2.9
    R-Sym I(Observed) 0.332
    Redundancy 1.5
    Number Unique Reflections(All) 32153
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.78
    Resolution(Low) 10.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 32153
    Number of Reflections(Observed) 28964
    Number of Reflections(R-Free) 3189
    Percent Reflections(Observed) 86.3
    R-Factor(All) 0.1989
    R-Factor(Observed) 0.1953
    R-Work 0.1953
    R-Free 0.239
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    s_approx_iso_adps 0.0
    s_similar_adp_cmpnt 0.075
    s_rigid_bond_adp_cmpnt 0.0
    s_anti_bump_dis_restr 0.059
    s_non_zero_chiral_vol 0.043
    s_zero_chiral_vol 0.034
    s_from_restr_planes 0.0272
    s_similar_dist 0.0
    s_angle_d 0.024
    s_bond_d 0.017
     
    Coordinate Error
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2319
    Nucleic Acid Atoms 0
    Heterogen Atoms 33
    Solvent Atoms 182
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) R-AXIS
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement SHELXL-97
     
    Software
    refinement SHELXL-97
    model building SHELX