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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3GKR
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details 30% PEG6000, 0.3M chlorure de sodium, 0.01M chlorure de magnesium, 0.07M sulfate d'ammonium, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 42.32 α = 90
    b = 101.84 β = 102.85
    c = 46.85 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Details MIRRORS
    Collection Date 2006-02-11
     
    Diffraction Radiation
    Monochromator SI111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE BM30A
    Wavelength List 0.97985
    Site ESRF
    Beamline BM30A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.6
    Resolution(Low) 27.2
    Number Reflections(All) 51014
    Number Reflections(Observed) 50198
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.033
    B(Isotropic) From Wilson Plot 22.2
    Redundancy 1.7
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.7
    Percent Possible(All) 96.2
    R Merge I(Observed) 0.139
    Mean I Over Sigma(Observed) 5.6
    R-Sym I(Observed) 0.139
    Redundancy 1.7
    Number Unique Reflections(All) 8475
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 27.2
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 50653
    Number of Reflections(Observed) 48120
    Number of Reflections(R-Free) 2533
    Percent Reflections(Observed) 100.0
    R-Factor(All) 0.17513
    R-Factor(Observed) 0.17513
    R-Work 0.17301
    R-Free 0.21561
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 13.912
    Anisotropic B[1][1] 0.4242
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0943
    Anisotropic B[2][2] 0.4196
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.4351
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.642
    Number of Reflections(Observed) 3700
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3510
    R-Factor(R-Work) 0.236
    R-Factor(R-Free) 0.298
    Percent Reflections(Observed) 96.2
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 5.217
    r_scbond_it 3.553
    r_mcangle_it 2.307
    r_mcbond_it 1.466
    r_gen_planes_refined 0.015
    r_chiral_restr 0.188
    r_dihedral_angle_4_deg 22.35
    r_dihedral_angle_3_deg 13.083
    r_dihedral_angle_2_deg 31.965
    r_dihedral_angle_1_deg 6.071
    r_angle_refined_deg 2.349
    r_bond_refined_d 0.029
     
    Coordinate Error
    Luzzati ESD(Observed) 0.153
    Luzzati Resolution Cutoff(Low) 6.0
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2764
    Nucleic Acid Atoms 0
    Heterogen Atoms 14
    Solvent Atoms 514
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0066
     
    Software
    refinement REFMAC version: 5.5.0066
    model building PHASER
    data collection MAR345dtb