POP-OUT | CLOSE

An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3KA3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 9
    Temperature 277.0
    Details 2M MgCl2, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 183.89 α = 90
    b = 183.89 β = 90
    c = 183.89 γ = 90
     
    Space Group
    Space Group Name:    F 4 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Details Mirror 1: plane parabola Pt and Rh-coated Invar steel. Mirror 2: torroid Pt and Rh-coated Si
     
    Diffraction Radiation
    Monochromator KOHZU: Double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.3.1
    Wavelength List 1.1159
    Site ALS
    Beamline 8.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.4
    Resolution(Low) 50
    Number Reflections(Observed) 52741
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.088
    Redundancy 13.6
     
    High Resolution Shell Details
    Resolution(High) 1.4
    Resolution(Low) 1.48
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.969
    Mean I Over Sigma(Observed) 0.8
    R-Sym I(Observed) 0.969
    Redundancy 13.7
    Number Unique Reflections(All) 7566
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.4
    Resolution(Low) 50.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 52741
    Number of Reflections(R-Free) 2689
    Percent Reflections(Observed) 99.99
    R-Factor(Observed) 0.137
    R-Work 0.136
    R-Free 0.159
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 16.983
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4
    Shell Resolution(Low) 1.436
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 3605
    R-Factor(R-Work) 0.398
    R-Factor(R-Free) 0.438
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 4.74
    r_sphericity_free 15.282
    r_rigid_bond_restr 2.7
    r_scangle_it 7.613
    r_scbond_it 5.375
    r_mcangle_it 3.026
    r_mcbond_other 0.964
    r_bond_refined_d 0.028
    r_bond_other_d 0.001
    r_angle_refined_deg 2.141
    r_angle_other_deg 1.724
    r_dihedral_angle_1_deg 4.754
    r_dihedral_angle_2_deg 38.192
    r_dihedral_angle_3_deg 14.292
    r_dihedral_angle_4_deg 15.94
    r_chiral_restr 0.137
    r_gen_planes_refined 0.013
    r_gen_planes_other 0.003
    r_mcbond_it 2.243
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1429
    Nucleic Acid Atoms 0
    Heterogen Atoms 17
    Solvent Atoms 292
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.4.0077
     
    Software
    data extraction pdb_extract version: 3.005
    refinement REFMAC5 version: 5.4.0077
    data processing SCALA version: 3.2.5
    reflection data processing Mosflm