POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
4IJN
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5.5
    Temperature 289.0
    Details MysmA.00640.a.A1 PS00601 at 20 mg/mL with 2 mM AMP and 2 mM MnCl2 against JCSG+ condition H7, 25% PEG 3350, 0.1 M BisTris, 0.2 M ammonium sulfate with 15% ethylene glycol as cryo-protectant, crystal tracking ID 238414h7, unique puck ID gpy2-6, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 55.43 α = 90
    b = 81.91 β = 96.51
    c = 95.4 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 RIGAKU SATURN 944+
    Details VariMax
    Collection Date 2012-11-24
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FR-E+ SUPERBRIGHT
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(All) 93194
    Number Reflections(Observed) 91223
    Percent Possible(Observed) 97.9
    R Merge I(Observed) 0.045
    B(Isotropic) From Wilson Plot 23.913
    Redundancy 4.6
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.74
    Percent Possible(All) 90.2
    R Merge I(Observed) 0.29
    Mean I Over Sigma(Observed) 3.22
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 45.74
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 91201
    Number of Reflections(R-Free) 4566
    Percent Reflections(Observed) 97.89
    R-Factor(Observed) 0.1747
    R-Work 0.1733
    R-Free 0.2015
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 19.5464
    Anisotropic B[1][1] -0.8
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.67
    Anisotropic B[2][2] 0.43
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.44
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.744
    Number of Reflections(R-Free) 328
    Number of Reflections(R-Work) 5886
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.255
    Percent Reflections(Observed) 90.24
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_mcangle_it 1.275
    r_mcbond_other 0.776
    r_bond_refined_d 0.011
    r_bond_other_d 0.001
    r_angle_refined_deg 1.484
    r_angle_other_deg 0.775
    r_dihedral_angle_1_deg 6.414
    r_dihedral_angle_2_deg 30.396
    r_dihedral_angle_3_deg 11.906
    r_dihedral_angle_4_deg 18.301
    r_chiral_restr 0.084
    r_gen_planes_refined 0.007
    r_gen_planes_other 0.001
    r_mcbond_it 0.777
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5570
    Nucleic Acid Atoms 0
    Heterogen Atoms 68
    Solvent Atoms 697
     
     
  •   Software and Computing Hide
    Computing
    Data Collection StructureStudio
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0032
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser version: 2.5.2
    data reduction Xscale