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X-RAY DIFFRACTION
Materials and Methods page
4HPV
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.6
    Temperature 298.0
    Details Protein Solution (6.8-13.5 mg/ml protein, 25mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 5.6) Cryoprotected with 20% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 151.3 α = 90
    b = 151.3 β = 90
    c = 221.15 γ = 120
     
    Space Group
    Space Group Name:    P 65 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2012-03-08
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2012-02-11
     
    Diffraction Radiation
    Monochromator Diamond [111]
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator Diamond [111]
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-G
    Wavelength List 0.97856
    Site APS
    Beamline 21-ID-G
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-G
    Wavelength List 0.97856
    Site APS
    Beamline 21-ID-G
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.21
    Resolution(Low) 50
    Number Reflections(All) 75422
    Number Reflections(Observed) 74442
    Percent Possible(Observed) 98.7
    R Merge I(Observed) 0.118
    B(Isotropic) From Wilson Plot 42.94
    Redundancy 19.9
     
    High Resolution Shell Details
    Resolution(High) 2.21
    Resolution(Low) 2.25
    Percent Possible(All) 76.6
    Redundancy 9.2
    Number Unique Reflections(All) 2830
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.214
    Resolution(Low) 49.526
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 74655
    Number of Reflections(Observed) 74289
    Number of Reflections(R-Free) 3730
    Percent Reflections(Observed) 99.51
    R-Factor(Observed) 0.2
    R-Work 0.199
    R-Free 0.2201
    R-Free Selection Details RAMDOM, ASSIGN TEST SET IN THIN RESOLUTION SHELLS
     
    Temperature Factor Modeling
    Mean Isotropic B Value 38.372
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2142
    Shell Resolution(Low) 2.2422
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 2274
    R-Factor(R-Work) 0.3097
    R-Factor(R-Free) 0.3698
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2422
    Shell Resolution(Low) 2.2717
    Number of Reflections(R-Work) 2680
    R-Factor(R-Work) 0.2835
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2717
    Shell Resolution(Low) 2.3029
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 2506
    R-Factor(R-Work) 0.2698
    R-Factor(R-Free) 0.3106
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3029
    Shell Resolution(Low) 2.3358
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2504
    R-Factor(R-Work) 0.2651
    R-Factor(R-Free) 0.2852
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3358
    Shell Resolution(Low) 2.3706
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2543
    R-Factor(R-Work) 0.2505
    R-Factor(R-Free) 0.288
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3706
    Shell Resolution(Low) 2.4077
    Number of Reflections(R-Work) 2722
    R-Factor(R-Work) 0.2387
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4077
    Shell Resolution(Low) 2.4471
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2543
    R-Factor(R-Work) 0.2341
    R-Factor(R-Free) 0.2831
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4471
    Shell Resolution(Low) 2.4893
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2517
    R-Factor(R-Work) 0.2286
    R-Factor(R-Free) 0.2678
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4893
    Shell Resolution(Low) 2.5346
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2542
    R-Factor(R-Work) 0.2244
    R-Factor(R-Free) 0.3007
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5346
    Shell Resolution(Low) 2.5833
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.2209
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5833
    Shell Resolution(Low) 2.6361
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2549
    R-Factor(R-Work) 0.22
    R-Factor(R-Free) 0.2635
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6361
    Shell Resolution(Low) 2.6934
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2528
    R-Factor(R-Work) 0.2148
    R-Factor(R-Free) 0.2483
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6934
    Shell Resolution(Low) 2.756
    Number of Reflections(R-Free) 54
    Number of Reflections(R-Work) 2701
    R-Factor(R-Work) 0.2102
    R-Factor(R-Free) 0.2518
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.756
    Shell Resolution(Low) 2.825
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2599
    R-Factor(R-Work) 0.2171
    R-Factor(R-Free) 0.2711
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.825
    Shell Resolution(Low) 2.9013
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2573
    R-Factor(R-Work) 0.208
    R-Factor(R-Free) 0.2504
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9013
    Shell Resolution(Low) 2.9867
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2560
    R-Factor(R-Work) 0.2134
    R-Factor(R-Free) 0.2145
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9867
    Shell Resolution(Low) 3.0831
    Number of Reflections(R-Work) 2751
    R-Factor(R-Work) 0.2093
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0831
    Shell Resolution(Low) 3.1932
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2566
    R-Factor(R-Work) 0.2077
    R-Factor(R-Free) 0.2452
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1932
    Shell Resolution(Low) 3.3211
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.1989
    R-Factor(R-Free) 0.2403
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3211
    Shell Resolution(Low) 3.4722
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2582
    R-Factor(R-Work) 0.1934
    R-Factor(R-Free) 0.2302
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4722
    Shell Resolution(Low) 3.6552
    Number of Reflections(R-Work) 2778
    R-Factor(R-Work) 0.1817
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6552
    Shell Resolution(Low) 3.8841
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2605
    R-Factor(R-Work) 0.1813
    R-Factor(R-Free) 0.1967
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8841
    Shell Resolution(Low) 4.1839
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1643
    R-Factor(R-Free) 0.1824
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1839
    Shell Resolution(Low) 4.6046
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2627
    R-Factor(R-Work) 0.1601
    R-Factor(R-Free) 0.1754
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6046
    Shell Resolution(Low) 5.2703
    Number of Reflections(R-Work) 2846
    R-Factor(R-Work) 0.1596
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2703
    Shell Resolution(Low) 6.6375
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.2198
    R-Factor(R-Free) 0.186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6375
    Shell Resolution(Low) 49.5382
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 2865
    R-Factor(R-Work) 0.2098
    R-Factor(R-Free) 0.1942
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 11.725
    f_plane_restr 0.002
    f_chiral_restr 0.048
    f_angle_d 0.685
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6192
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 304
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX: PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL