POP-OUT | CLOSE

An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2CYG
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.6
    Temperature 293.0
    Details Sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.27 α = 90
    b = 53.93 β = 90
    c = 113.55 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 4
    Collection Date 2002-12-04
     
    Diffraction Radiation
    Monochromator single wavelength
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength List 0.933
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.45
    Resolution(Low) 20
    Number Reflections(All) 53238
    Number Reflections(Observed) 52014
    Percent Possible(Observed) 97.7
    R Merge I(Observed) 0.035
    B(Isotropic) From Wilson Plot 10.46
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 1.45
    Resolution(Low) 1.5
    Percent Possible(All) 97.7
    R Merge I(Observed) 0.129
    Mean I Over Sigma(Observed) 5.6
    R-Sym I(Observed) 0.129
    Redundancy 3.6
    Number Unique Reflections(All) 4819
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.45
    Resolution(Low) 20.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 52014
    Number of Reflections(Observed) 49317
    Number of Reflections(R-Free) 2644
    Percent Reflections(Observed) 97.4
    R-Factor(All) 0.15835
    R-Factor(Observed) 0.15835
    R-Work 0.15722
    R-Free 0.1794
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 14.92
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.45
    Shell Resolution(Low) 1.487
    Number of Reflections(Observed) 3416
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3416
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.189
    Percent Reflections(Observed) 0.05
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.938
    r_scbond_it 1.206
    r_mcangle_it 0.761
    r_mcbond_it 0.384
    r_symmetry_hbond_refined 0.124
    r_symmetry_vdw_other 0.188
    r_symmetry_vdw_refined 0.097
    r_bond_refined_d 0.006
    r_bond_other_d 0.002
    r_angle_refined_deg 1.095
    r_angle_other_deg 0.787
    r_dihedral_angle_1_deg 6.01
    r_chiral_restr 0.067
    r_gen_planes_refined 0.004
    r_gen_planes_other 0.001
    r_nbd_refined 0.195
    r_nbd_other 0.229
    r_nbtor_other 0.078
    r_xyhbond_nbd_refined 0.118
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2364
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 407
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution AMORE
    Structure Refinement REFMAC 5.1.19
     
    Software
    refinement REFMAC version: 5.1.19