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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3ERQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 277.0
    Details 22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, Soaked in higher % MPD before freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 30.98 α = 90
    b = 60.28 β = 93.43
    c = 37.96 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 110
     
    Diffraction Detector
    Detector CCD
    Type BRUKER APEX II
    Details multi-layer optics
    Collection Date 2008-06-15
     
    Diffraction Radiation
    Monochromator GE111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SEALED TUBE
    Type OTHER
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.1
    Resolution(Low) 60.28
    Number Reflections(All) 8220
    Number Reflections(Observed) 8216
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.0816
    B(Isotropic) From Wilson Plot 38.6
    Redundancy 15.45
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.2
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.388
    Mean I Over Sigma(Observed) 4.49
    R-Sym I(Observed) 0.2114
    Redundancy 11.86
    Number Unique Reflections(All) 1058
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 23.29
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 8181
    Number of Reflections(Observed) 8181
    Number of Reflections(R-Free) 803
    Percent Reflections(Observed) 99.78
    R-Factor(All) 0.215
    R-Factor(Observed) 0.215
    R-Work 0.209
    R-Free 0.278
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.224
    Anisotropic B[1][1] -0.05
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.01
    Anisotropic B[2][2] 0.01
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.04
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.154
    Number of Reflections(Observed) 585
    Number of Reflections(R-Free) 60
    Number of Reflections(R-Work) 521
    R-Factor(R-Work) 0.303
    R-Factor(R-Free) 0.365
    Percent Reflections(Observed) 99.316
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.154
    Shell Resolution(Low) 2.213
    Number of Reflections(Observed) 600
    Number of Reflections(R-Free) 67
    R-Factor(R-Work) 0.247
    R-Factor(R-Free) 0.35
    Percent Reflections(Observed) 99.5
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.216
    Shell Resolution(Low) 2.276
    Number of Reflections(Observed) 548
    Number of Reflections(R-Free) 61
    R-Factor(R-Work) 0.244
    R-Factor(R-Free) 0.327
    Percent Reflections(Observed) 99.635
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.276
    Shell Resolution(Low) 2.346
    Number of Reflections(Observed) 563
    Number of Reflections(R-Free) 65
    R-Factor(R-Work) 0.243
    R-Factor(R-Free) 0.354
    Percent Reflections(Observed) 99.467
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.346
    Shell Resolution(Low) 2.422
    Number of Reflections(Observed) 527
    Number of Reflections(R-Free) 53
    R-Factor(R-Work) 0.249
    R-Factor(R-Free) 0.384
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.422
    Shell Resolution(Low) 2.506
    Number of Reflections(Observed) 529
    Number of Reflections(R-Free) 46
    R-Factor(R-Work) 0.249
    R-Factor(R-Free) 0.338
    Percent Reflections(Observed) 99.811
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.985
    r_scbond_it 2.636
    r_mcangle_it 1.683
    r_mcbond_it 0.934
    r_gen_planes_refined 0.008
    r_chiral_restr 0.095
    r_dihedral_angle_4_deg 14.772
    r_dihedral_angle_3_deg 17.072
    r_dihedral_angle_2_deg 33.39
    r_dihedral_angle_1_deg 7.064
    r_angle_refined_deg 1.216
    r_bond_refined_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1034
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 45
     
     
  •   Software and Computing Hide
    Computing
    Data Collection APEX
    Data Reduction (intensity integration) SAINT
    Data Reduction (data scaling) SAINT
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0036
     
    Software
    data extraction pdb_extract version: 3.006
    refinement REFMAC5 version: 5.5.0036
    molecular replacement Phaser
    collection/data indexing SAINT