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X-RAY DIFFRACTION
Materials and Methods page
2PMQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 8.5
    Temperature 294.0
    Details 100mM Tris-HCl pH 8.5, 25% PEG 3350, 200mM Magnesium chloride, VAPOR DIFFUSION, temperature 294K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 136.38 α = 90
    b = 136.38 β = 90
    c = 80.93 γ = 90
     
    Space Group
    Space Group Name:    P 4 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Collection Date 2007-04-08
     
    Diffraction Radiation
    Monochromator diamond
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 31-ID
    Wavelength List 0.97958
    Site APS
    Beamline 31-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.72
    Resolution(Low) 96.44
    Number Reflections(All) 81085
    Number Reflections(Observed) 81085
    Percent Possible(Observed) 98.9
    R Merge I(Observed) 0.086
    B(Isotropic) From Wilson Plot 17.8
    Redundancy 12.0
     
    High Resolution Shell Details
    Resolution(High) 1.72
    Resolution(Low) 1.81
    Percent Possible(All) 93.0
    R Merge I(Observed) 0.306
    Mean I Over Sigma(Observed) 6.1
    R-Sym I(Observed) 0.306
    Redundancy 10.9
    Number Unique Reflections(All) 10981
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.72
    Resolution(Low) 20.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 81006
    Number of Reflections(Observed) 81006
    Number of Reflections(R-Free) 4061
    Percent Reflections(Observed) 99.7
    R-Factor(Observed) 0.167
    R-Work 0.165
    R-Free 0.191
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 15.922
    Anisotropic B[1][1] 0.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.04
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.72
    Shell Resolution(Low) 1.76
    Number of Reflections(Observed) 5709
    Number of Reflections(R-Free) 293
    Number of Reflections(R-Work) 5416
    R-Factor(R-Work) 0.185
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 96.52
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.319
    r_scbond_it 2.364
    r_mcangle_it 1.338
    r_mcbond_other 0.22
    r_mcbond_it 1.154
    r_symmetry_hbond_refined 0.16
    r_symmetry_vdw_other 0.356
    r_symmetry_vdw_refined 0.315
    r_xyhbond_nbd_refined 0.144
    r_nbtor_other 0.086
    r_nbtor_refined 0.177
    r_nbd_other 0.204
    r_bond_refined_d 0.012
    r_bond_other_d 0.002
    r_angle_refined_deg 1.341
    r_angle_other_deg 0.902
    r_dihedral_angle_1_deg 7.483
    r_dihedral_angle_2_deg 31.606
    r_dihedral_angle_3_deg 11.735
    r_dihedral_angle_4_deg 16.782
    r_chiral_restr 0.081
    r_gen_planes_refined 0.006
    r_gen_planes_other 0.001
    r_nbd_refined 0.222
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5626
    Nucleic Acid Atoms 0
    Heterogen Atoms 5
    Solvent Atoms 687
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR CCD
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution SHELXC, SHELXD, SHELXE
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 2.000
    refinement REFMAC5
    data processing SCALA