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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4HVD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 293.0
    Details 30% PEG3350, 0.1M MES, 0.2M MgCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 46.82 α = 90
    b = 75.42 β = 90
    c = 89.39 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 315r
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-2
    Wavelength List 0.97929
    Site SSRL
    Beamline BL9-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.85
    Resolution(Low) 44.68
    Number Reflections(Observed) 21755
    Percent Possible(Observed) 82.73
    B(Isotropic) From Wilson Plot 26.6
    Redundancy 4.7
     
    High Resolution Shell Details
    Resolution(High) 1.85
    Resolution(Low) 1.9
    Percent Possible(All) 17.0
    Mean I Over Sigma(Observed) 2.3
    R-Sym I(Observed) 0.263
    Redundancy 1.5
    Number Unique Reflections(All) 340
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.85
    Resolution(Low) 34.74
    Number of Reflections(Observed) 21755
    Number of Reflections(R-Free) 1167
    Percent Reflections(Observed) 82.73
    R-Factor(Observed) 0.22466
    R-Work 0.22285
    R-Free 0.25918
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 35.014
    Anisotropic B[1][1] 1.46
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.25
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.21
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.85
    Shell Resolution(Low) 1.898
    Number of Reflections(R-Free) 16
    Number of Reflections(R-Work) 323
    R-Factor(R-Work) 0.297
    R-Factor(R-Free) 0.277
    Percent Reflections(Observed) 17.04
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.028
    r_scbond_it 1.23
    r_mcangle_it 0.992
    r_mcbond_it 0.561
    r_nbd_refined 0.178
    r_gen_planes_refined 0.003
    r_chiral_restr 0.067
    r_dihedral_angle_4_deg 16.65
    r_dihedral_angle_3_deg 14.544
    r_dihedral_angle_2_deg 33.894
    r_dihedral_angle_1_deg 4.751
    r_angle_refined_deg 0.976
    r_bond_refined_d 0.007
    r_nbtor_refined 0.304
    r_xyhbond_nbd_refined 0.123
    r_symmetry_vdw_refined 0.152
    r_symmetry_hbond_refined 0.112
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2215
    Nucleic Acid Atoms 0
    Heterogen Atoms 31
    Solvent Atoms 131
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building Phaser
    data collection ADSC version: Quantum