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X-RAY DIFFRACTION
Materials and Methods page
4IA5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.9
    Temperature 298.0
    Details 37% MPD, 0.1M Hepes/KOH, 10mM Phenol, 3.6mM linoleic acid, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 168.75 α = 90
    b = 78.97 β = 90
    c = 108.77 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2008-12-19
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type BESSY BEAMLINE 14.1
    Wavelength List 0.98140
    Site BESSY
    Beamline 14.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.22
    Resolution(Low) 50
    Number Reflections(Observed) 122663
    Percent Possible(Observed) 88.4
    R Merge I(Observed) 0.045
    B(Isotropic) From Wilson Plot 39.164
    Redundancy 3.05
     
    High Resolution Shell Details
    Resolution(High) 2.22
    Resolution(Low) 2.32
    Percent Possible(All) 55.6
    R Merge I(Observed) 0.187
    Mean I Over Sigma(Observed) 3.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.22
    Resolution(Low) 44.791
    Cut-off Sigma(F) 0.87
    Number of Reflections(Observed) 122595
    Number of Reflections(R-Free) 6159
    Percent Reflections(Observed) 88.38
    R-Factor(Observed) 0.2161
    R-Work 0.2138
    R-Free 0.2585
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 64.7363
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.22
    Shell Resolution(Low) 2.2453
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 2089
    R-Factor(R-Work) 0.3178
    R-Factor(R-Free) 0.3656
    Percent Reflections(Observed) 48.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2453
    Shell Resolution(Low) 2.2717
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2411
    R-Factor(R-Work) 0.321
    R-Factor(R-Free) 0.4089
    Percent Reflections(Observed) 55.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2717
    Shell Resolution(Low) 2.2994
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2547
    R-Factor(R-Work) 0.3047
    R-Factor(R-Free) 0.4254
    Percent Reflections(Observed) 59.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2994
    Shell Resolution(Low) 2.3285
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2858
    R-Factor(R-Work) 0.3023
    R-Factor(R-Free) 0.3306
    Percent Reflections(Observed) 65.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3285
    Shell Resolution(Low) 2.3591
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3059
    R-Factor(R-Work) 0.3033
    R-Factor(R-Free) 0.303
    Percent Reflections(Observed) 70.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3591
    Shell Resolution(Low) 2.3914
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 3238
    R-Factor(R-Work) 0.3002
    R-Factor(R-Free) 0.3401
    Percent Reflections(Observed) 74.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3914
    Shell Resolution(Low) 2.4256
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3492
    R-Factor(R-Work) 0.3033
    R-Factor(R-Free) 0.3601
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4256
    Shell Resolution(Low) 2.4618
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3587
    R-Factor(R-Work) 0.2922
    R-Factor(R-Free) 0.3429
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4618
    Shell Resolution(Low) 2.5003
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 3720
    R-Factor(R-Work) 0.2793
    R-Factor(R-Free) 0.3358
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5003
    Shell Resolution(Low) 2.5413
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 3984
    R-Factor(R-Work) 0.2814
    R-Factor(R-Free) 0.335
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5413
    Shell Resolution(Low) 2.5851
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 3987
    R-Factor(R-Work) 0.2732
    R-Factor(R-Free) 0.3325
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5851
    Shell Resolution(Low) 2.6321
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 4188
    R-Factor(R-Work) 0.2673
    R-Factor(R-Free) 0.3154
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6321
    Shell Resolution(Low) 2.6827
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4149
    R-Factor(R-Work) 0.2642
    R-Factor(R-Free) 0.3537
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6827
    Shell Resolution(Low) 2.7374
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4320
    R-Factor(R-Work) 0.2722
    R-Factor(R-Free) 0.2863
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7374
    Shell Resolution(Low) 2.797
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4315
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.2519
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.797
    Shell Resolution(Low) 2.862
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4357
    R-Factor(R-Work) 0.2549
    R-Factor(R-Free) 0.3209
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.862
    Shell Resolution(Low) 2.9336
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4319
    R-Factor(R-Work) 0.2515
    R-Factor(R-Free) 0.3239
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9336
    Shell Resolution(Low) 3.0129
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4328
    R-Factor(R-Work) 0.2467
    R-Factor(R-Free) 0.3326
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0129
    Shell Resolution(Low) 3.1015
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4270
    R-Factor(R-Work) 0.2422
    R-Factor(R-Free) 0.3013
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1015
    Shell Resolution(Low) 3.2016
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4325
    R-Factor(R-Work) 0.2257
    R-Factor(R-Free) 0.2698
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2016
    Shell Resolution(Low) 3.316
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 4309
    R-Factor(R-Work) 0.2173
    R-Factor(R-Free) 0.2927
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.316
    Shell Resolution(Low) 3.4487
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4360
    R-Factor(R-Work) 0.2122
    R-Factor(R-Free) 0.2329
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4487
    Shell Resolution(Low) 3.6056
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 4282
    R-Factor(R-Work) 0.1901
    R-Factor(R-Free) 0.235
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6056
    Shell Resolution(Low) 3.7956
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4274
    R-Factor(R-Work) 0.187
    R-Factor(R-Free) 0.2378
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7956
    Shell Resolution(Low) 4.0333
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4314
    R-Factor(R-Work) 0.1716
    R-Factor(R-Free) 0.1919
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0333
    Shell Resolution(Low) 4.3444
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 4320
    R-Factor(R-Work) 0.1592
    R-Factor(R-Free) 0.1981
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3444
    Shell Resolution(Low) 4.7812
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4280
    R-Factor(R-Work) 0.1563
    R-Factor(R-Free) 0.2166
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7812
    Shell Resolution(Low) 5.472
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4273
    R-Factor(R-Work) 0.1672
    R-Factor(R-Free) 0.2126
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.472
    Shell Resolution(Low) 6.8901
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4250
    R-Factor(R-Work) 0.1869
    R-Factor(R-Free) 0.2012
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8901
    Shell Resolution(Low) 44.7999
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4231
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.2066
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.185
    f_plane_restr 0.006
    f_chiral_restr 0.08
    f_angle_d 1.194
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9367
    Nucleic Acid Atoms 0
    Heterogen Atoms 90
    Solvent Atoms 473
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution SHELXD
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    phasing SHELX
    data reduction Xscale