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An Information Portal to 109822 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DNQ
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 6.6
    Temperature 291.0
    Details (NH4)2HPO4 0.2M, PEG 3350 18%, pH 6.6, vapor diffusion, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 176.66 α = 90
    b = 176.66 β = 90
    c = 107.67 γ = 120
     
    Space Group
    Space Group Name:    P 31
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-07-23
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type AUSTRALIAN SYNCHROTRON BEAMLINE MX2
    Wavelength List 0.978916
    Site AUSTRALIAN SYNCHROTRON
    Beamline MX2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.8
    Resolution(Low) 62.36
    Number Reflections(All) 92560
    Number Reflections(Observed) 92560
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.182
    B(Isotropic) From Wilson Plot 56.6
    Redundancy 11.1
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.95
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.53
    Mean I Over Sigma(Observed) 4.5
    R-Sym I(Observed) 0.53
    Redundancy 10.9
    Number Unique Reflections(All) 13513
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.8
    Resolution(Low) 62.36
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 92536
    Number of Reflections(R-Free) 4632
    Percent Reflections(Observed) 99.99
    R-Factor(Observed) 0.2437
    R-Work 0.2423
    R-Free 0.2715
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 52.6304
    Anisotropic B[1][1] -0.4
    Anisotropic B[1][2] -0.2
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.4
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.6
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8
    Shell Resolution(Low) 2.873
    Number of Reflections(R-Free) 314
    Number of Reflections(R-Work) 6554
    R-Factor(R-Work) 0.264
    R-Factor(R-Free) 0.314
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.509
    r_scbond_it 1.023
    r_mcangle_it 0.611
    r_mcbond_it 0.329
    r_gen_planes_refined 0.005
    r_chiral_restr 0.099
    r_dihedral_angle_4_deg 23.14
    r_dihedral_angle_3_deg 18.336
    r_dihedral_angle_2_deg 27.878
    r_dihedral_angle_1_deg 5.795
    r_angle_refined_deg 1.463
    r_bond_refined_d 0.015
     
    Coordinate Error
    Luzzati ESD(R-Free Set) 0.437
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 24719
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 323
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Blu-Ice
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser version: 2.1.4
    data reduction SCALA version: 3.3.16
    data collection Mosflm