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X-RAY DIFFRACTION
Materials and Methods page
1YHM
  •   Crystallization Hide
    Crystallization Experiments
    Method LIQUID DIFFUSION
    pH 4.6
    Temperature 293.0
    Details peg 4000 Na acetate amonium sulfate, pH 4.6, LIQUID DIFFUSION, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 103.21 α = 90
    b = 103.21 β = 90
    c = 385.24 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2004-06-16
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.3
    Resolution(Low) 87.71
    Number Reflections(Observed) 55148
    R Merge I(Observed) 0.146
    Redundancy 12.9
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.38
    Percent Possible(All) 95.6
    R Merge I(Observed) 0.895
    Redundancy 6.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 87.71
    Number of Reflections(Observed) 40998
    Number of Reflections(R-Free) 2189
    Percent Reflections(Observed) 99.86
    R-Factor(Observed) 0.2114
    R-Work 0.20798
    R-Free 0.2777
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 42.193
    Anisotropic B[1][1] 1.5
    Anisotropic B[1][2] 0.75
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.5
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.26
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.565
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2957
    R-Factor(R-Work) 0.297
    R-Factor(R-Free) 0.345
    Percent Reflections(Observed) 99.97
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.93
    r_scbond_it 2.91
    r_mcangle_it 1.397
    r_mcbond_it 1.509
    r_nbd_refined 0.25
    r_gen_planes_refined 0.007
    r_chiral_restr 0.182
    r_dihedral_angle_4_deg 23.692
    r_dihedral_angle_3_deg 19.417
    r_dihedral_angle_2_deg 42.897
    r_dihedral_angle_1_deg 6.06
    r_angle_refined_deg 1.981
    r_bond_refined_d 0.019
    r_nbtor_refined 0.32
    r_xyhbond_nbd_refined 0.176
    r_metal_ion_refined 0.153
    r_symmetry_vdw_refined 0.273
    r_symmetry_hbond_refined 0.104
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8673
    Nucleic Acid Atoms 0
    Heterogen Atoms 108
    Solvent Atoms 110
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL
    Structure Solution AMORE
    Structure Refinement REFMAC 5.2.0005
     
    Software
    data extraction pdb_extract version: 1.501
    refinement REFMAC5
    data processing HKL