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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3TXD
  •   Crystallization Hide
    Crystallization Experiments
    Method BATCH
    pH 4.7
    Temperature 295.0
    Details 49 mg HEWL + 3.13 mg carboplatin in 1 mL 0.04 M sodium acetate + 1 mL 10% sodium chloride, with glycerol as cryoprotectant, pH 4.7, BATCH, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 78.87 α = 90
    b = 78.87 β = 90
    c = 36.98 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU RAXIS IV
    Details Osmic Confocal Max-Flux, blue configuration
    Collection Date 2010-03-02
     
    Diffraction Radiation
    Monochromator NONE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 4.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.53
    Resolution(Low) 55.77
    Number Reflections(All) 18093
    Number Reflections(Observed) 15683
    Percent Possible(Observed) 86.6
    R Merge I(Observed) 0.076
    B(Isotropic) From Wilson Plot 29.6
    Redundancy 11.98
     
    High Resolution Shell Details
    Resolution(High) 1.53
    Resolution(Low) 1.59
    Percent Possible(All) 91.4
    R Merge I(Observed) 0.327
    Mean I Over Sigma(Observed) 2.1
    Redundancy 2.51
    Number Unique Reflections(All) 18093
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.53
    Resolution(Low) 55.77
    Cut-off Sigma(I) 2.0
    Cut-off Sigma(F) 4.0
    Number of Reflections(all) 18093
    Number of Reflections(Observed) 15683
    Number of Reflections(R-Free) 847
    Percent Reflections(Observed) 91.38
    R-Factor(All) 0.2086
    R-Factor(Observed) 0.20228
    R-Work 0.19946
    R-Free 0.25826
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 35.168
    Anisotropic B[1][1] 0.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.04
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.53
    Shell Resolution(Low) 1.572
    Number of Reflections(R-Free) 26
    Number of Reflections(R-Work) 409
    R-Factor(R-Work) 0.387
    R-Factor(R-Free) 0.313
    Percent Reflections(Observed) 33.51
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.396
    r_scbond_it 2.805
    r_mcangle_it 1.751
    r_mcbond_it 1.063
    r_gen_planes_refined 0.009
    r_chiral_restr 0.125
    r_dihedral_angle_4_deg 15.134
    r_dihedral_angle_3_deg 13.331
    r_dihedral_angle_2_deg 37.167
    r_dihedral_angle_1_deg 6.685
    r_angle_refined_deg 1.735
    r_bond_refined_d 0.021
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1001
    Nucleic Acid Atoms 0
    Heterogen Atoms 89
    Solvent Atoms 106
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) d*TREK
    Data Reduction (data scaling) d*TREK
    Structure Solution PHASER MOLECULAR REPLACEMENT
    Structure Refinement REFMAC 5.5.0110
     
    Software
    refinement REFMAC version: 5.5.0110
    model building PHASER version: MOLECULAR REPLACEMENT
    data collection CrystalClear