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X-RAY DIFFRACTION
Materials and Methods page
3ZD5
  •   Crystallization Hide
    Crystallization Experiments
    Details THE ENZYME AND SUBSTRATE WERE MIXED IN EQUIMOLAR AMOUNTS IN A SOLUTION CONTAINING 50 MM MES PH 5.5, 1.5 MM EDTA. THE COMPLEX WAS FORMED BY INCUBATING THE MIXTURE AT 95C FOR 2 MIN., THEN AT 65C FOR 2 MIN., AND FINALLY AT 27C FOR 5 MIN. 1 MM MGCL2 WAS INCLUDED IN THE MIXTURE BEFORE THE FINAL INCUBATION STEP. A 10 MG/ML CONCENTRATION OF RNA WAS USED FOR THE CRYSTALLIZATION EXPERIMENTS. THE RESERVOIR SOLUTION CONTAINED 0.5M (NH4)2SO4, 100 MM MES PH 6.5, AND 35% PEG 3350. AFTER MIXING THE RESERVOIR SOLUTION, THE SALT AND PEG PHASES WERE ALLOWED TO SEPARATE, AND ONLY THE SALT PHASE WAS USED FOR THE DROPS. THE CRYSTALS GREW IN HANGING DROPS OF 2 MICROLITERS AFTER 12 MONTHS OF INCUBATION AT 28C. THE CRYSTALS WERE WASHED IN THE SALT PHASE OF THE RESERVOIR SOLUTION PRIOR TO CRYO-FREEZING.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 49.89 α = 90
    b = 69.21 β = 111.83
    c = 60.08 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD (QUANTUM 315)
    Type ADSC
    Collection Date 2006-02-27
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-1
    Wavelength List 0.919, 0.920, 0.9266
    Site SSRL
    Beamline BL9-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.2
    Resolution(Low) 55.73
    Number Reflections(Observed) 9712
    Percent Possible(Observed) 99.2
    R Merge I(Observed) 0.04
    B(Isotropic) From Wilson Plot 43.18
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.32
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.22
    Mean I Over Sigma(Observed) 4.9
    Redundancy 4.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 2.2
    Resolution(Low) 20.22
    Cut-off Sigma(F) 1.5
    Number of Reflections(Observed) 9615
    Number of Reflections(R-Free) 935
    Percent Reflections(Observed) 99.13
    R-Factor(Observed) 0.1805
    R-Work 0.1768
    R-Free 0.2117
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2004
    Shell Resolution(Low) 2.3162
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1246
    R-Factor(R-Work) 0.2441
    R-Factor(R-Free) 0.306
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3162
    Shell Resolution(Low) 2.4611
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1217
    R-Factor(R-Work) 0.2366
    R-Factor(R-Free) 0.2735
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4611
    Shell Resolution(Low) 2.6507
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1255
    R-Factor(R-Work) 0.2468
    R-Factor(R-Free) 0.3087
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6507
    Shell Resolution(Low) 2.9168
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 1247
    R-Factor(R-Work) 0.253
    R-Factor(R-Free) 0.3115
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9168
    Shell Resolution(Low) 3.3372
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1254
    R-Factor(R-Work) 0.1929
    R-Factor(R-Free) 0.2504
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3372
    Shell Resolution(Low) 4.1983
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1239
    R-Factor(R-Work) 0.147
    R-Factor(R-Free) 0.1994
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1983
    Shell Resolution(Low) 20.2209
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1222
    R-Factor(R-Work) 0.1273
    R-Factor(R-Free) 0.133
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.039
    f_dihedral_angle_d 15.306
    f_angle_d 0.937
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 0
    Nucleic Acid Atoms 1346
    Heterogen Atoms 0
    Solvent Atoms 34
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) ADSC
    Data Reduction (data scaling) MOSFLM
    Structure Solution CNS
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building CNS