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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3ZIA
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.5
    Details ACTIVE F1-ATPASE (12 MG/ML) WAS EXCHANGED ON A DESALTING COLUMN INTO CRYSTALLISATION BUFFER, PREPARED IN D2O CONSISTING OF 100 MM BIS-TRIS PROPANE, PH 7.5, 100 MM SUCROSE, 1 MM ADP AND 10 MM MAGNESIUM SULPHATE. THEN THE ENZYME WAS INHIBITED AT 23C WITH A 4-FOLD MOLAR EXCESS OF YI1-53 (MUTATION E21A) IN THE PRESENCE OF 1 MM ATP AND 2 MM MAGNESIUM SULPHATE. FURTHER PORTIONS (5 UL OF A NEUTRALISED STOCK SOLUTION CONTAINING 200 MM ATP AND 400 MM MAGNESIUM SULPHATE/ML PROTEIN SOLUTION) WERE ADDED AFTER 5 AND 10 MIN. MORE THAN 95% OF THE ATP HYDROLYSIS ACTIVITY OF THE ENZYME WAS INHIBITED. SODIUM-POTASSIUM TARTRATE WAS ADDED TO 100 MM, AND THE CONCENTRATION OF THE PROTEIN SOLUTION WAS ADJUSTED TO 10 MG/ML WITH CRYSTALLISATION BUFFER. CRYSTALS WERE GROWN AT 23C IN 72 WELL MICRO-BATCH PLATES UNDER FILTERED PARAFFIN OIL. THE CRYSTALLISATION DROPS (4 UL) CONTAINED A 1:1 MIXTURE OF PROTEIN SOLUTION AND PRECIPITANT SOLUTION (20%-26% POLYETHYLENE GLYCOL 3000 AND 600 MM NACL PREPARED IN D2O).
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 118.22 α = 90
    b = 187.85 β = 89.96
    c = 181.81 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2009-10-15
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I24
    Wavelength 0.977
    Site DIAMOND
    Beamline I24
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 2.5
    Resolution(Low) 43.84
    Number Reflections(Observed) 268620
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.11
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.64
    Percent Possible(All) 97.6
    R Merge I(Observed) 0.75
    Mean I Over Sigma(Observed) 2.0
    Redundancy 3.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 181.81
    Number of Reflections(Observed) 254974
    Number of Reflections(R-Free) 13570
    Percent Reflections(Observed) 98.25
    R-Factor(Observed) 0.22618
    R-Work 0.2243
    R-Free 0.26194
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 60.332
    Anisotropic B[1][1] 0.18
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.46
    Anisotropic B[2][2] 0.66
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.84
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.565
    Number of Reflections(R-Free) 996
    Number of Reflections(R-Work) 18559
    R-Factor(R-Work) 0.335
    R-Factor(R-Free) 0.36
    Percent Reflections(Observed) 96.87
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.592
    r_scbond_it 2.688
    r_mcangle_it 1.084
    r_mcbond_it 0.576
    r_gen_planes_refined 0.004
    r_chiral_restr 0.075
    r_dihedral_angle_4_deg 16.409
    r_dihedral_angle_3_deg 16.365
    r_dihedral_angle_2_deg 35.082
    r_dihedral_angle_1_deg 5.472
    r_angle_refined_deg 1.175
    r_bond_refined_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 50724
    Nucleic Acid Atoms 0
    Heterogen Atoms 366
    Solvent Atoms 773
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) IMOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0110
     
    Software
    refinement REFMAC version: 5.5.0110
    model building PHASER