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An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VNA
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 293.0
    Details Ammonium sulfate, Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 37.01 α = 90
    b = 60.97 β = 90
    c = 67.38 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 RIGAKU
     
    Diffraction Radiation
    Monochromator 180 degree
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2
    Resolution(Low) 50
    Number Reflections(All) 10308
    Number Reflections(Observed) 10112
    Percent Possible(Observed) 98.1
    R Merge I(Observed) 0.073
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.05
    Percent Possible(All) 93.5
    R Merge I(Observed) 0.37
    Mean I Over Sigma(Observed) 5.6
    Redundancy 6.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 45.22
    Number of Reflections(Observed) 10112
    Number of Reflections(R-Free) 511
    Percent Reflections(Observed) 98.03
    R-Factor(Observed) 0.18807
    R-Work 0.18501
    R-Free 0.25147
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 23.293
    Anisotropic B[1][1] 0.24
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.5
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.25
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.998
    Shell Resolution(Low) 2.049
    Number of Reflections(R-Free) 37
    Number of Reflections(R-Work) 710
    R-Factor(R-Work) 0.223
    R-Factor(R-Free) 0.38
    Percent Reflections(Observed) 93.96
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.858
    r_scbond_it 2.379
    r_mcangle_it 1.324
    r_mcbond_it 0.934
    r_symmetry_hbond_refined 0.175
    r_bond_refined_d 0.014
    r_angle_refined_deg 1.302
    r_dihedral_angle_1_deg 5.559
    r_dihedral_angle_2_deg 38.752
    r_dihedral_angle_3_deg 15.113
    r_dihedral_angle_4_deg 21.04
    r_chiral_restr 0.083
    r_gen_planes_refined 0.005
    r_nbd_refined 0.205
    r_nbtor_refined 0.294
    r_xyhbond_nbd_refined 0.139
    r_symmetry_vdw_refined 0.152
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1154
    Nucleic Acid Atoms 0
    Heterogen Atoms 25
    Solvent Atoms 102
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building PHASES
    data collection HKL-2000