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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3KFR
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 5.8
    Temperature 277.0
    Details 0.5 M KSCN, 0.1 M MES-HCL, pH 5.8, 10% DMSO, VAPOR DIFFUSION, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 28.72 α = 90
    b = 65.57 β = 90
    c = 92.36 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
    Details Rh coated flat mirror
    Collection Date 2008-12-08
     
    Diffraction Radiation
    Monochromator Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL7-1
    Wavelength List 0.97946
    Site SSRL
    Beamline BL7-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.15
    Resolution(Low) 25.3
    Number Reflections(All) 63048
    Number Reflections(Observed) 61661
    Percent Possible(Observed) 97.8
    R Merge I(Observed) 0.051
    B(Isotropic) From Wilson Plot 12.0
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.15
    Resolution(Low) 1.18
    Percent Possible(All) 96.6
    R Merge I(Observed) 0.8
    Mean I Over Sigma(Observed) 0.9
    R-Sym I(Observed) 0.8
    Redundancy 3.9
    Number Unique Reflections(All) 4432
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.3
    Resolution(Low) 25.3
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 42972
    Number of Reflections(R-Free) 2151
    Percent Reflections(Observed) 98.0
    R-Factor(Observed) 0.184
    R-Work 0.183
    R-Free 0.207
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Anisotropic
    Mean Isotropic B Value 16.693
    Anisotropic B[1][1] 0.09
    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] -0.07
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3
    Shell Resolution(Low) 1.334
    Number of Reflections(Observed) 2915
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2915
    R-Factor(R-Work) 0.212
    R-Factor(R-Free) 0.263
    Percent Reflections(Observed) 97.65
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 3.197
    r_sphericity_free 4.003
    r_rigid_bond_restr 1.29
    r_bond_refined_d 0.01
    r_angle_refined_deg 1.437
    r_dihedral_angle_1_deg 6.481
    r_dihedral_angle_2_deg 36.783
    r_dihedral_angle_3_deg 10.527
    r_dihedral_angle_4_deg 13.812
    r_chiral_restr 0.086
    r_gen_planes_refined 0.007
    r_mcbond_it 1.182
    r_mcangle_it 1.928
    r_scbond_it 2.434
    r_scangle_it 3.801
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1520
    Nucleic Acid Atoms 0
    Heterogen Atoms 86
    Solvent Atoms 169
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Blu-ice
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution Molrep
    Structure Refinement REFMAC 5.5.0090
     
    Software
    data extraction pdb_extract version: 3.005
    refinement REFMAC5 version: 5.5.0090