POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4HPS
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 293.0
    Details 0.8 M Lithium Chloride, 0.1 M Tris:HCl, 32% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 77.06 α = 90
    b = 73.34 β = 111.96
    c = 80.54 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-09-21
     
    Diffraction Radiation
    Monochromator ROSENBAUM-ROCK DOUBLE CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.55
    Resolution(Low) 50
    Number Reflections(All) 115820
    Number Reflections(Observed) 115757
    Percent Possible(Observed) 96.1
    R Merge I(Observed) 0.055
    B(Isotropic) From Wilson Plot 19.8
    Redundancy 5.7
     
    High Resolution Shell Details
    Resolution(High) 1.55
    Resolution(Low) 1.58
    Percent Possible(All) 94.0
    R Merge I(Observed) 0.8
    Redundancy 5.7
    Number Unique Reflections(All) 5637
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.55
    Resolution(Low) 39.762
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 115697
    Number of Reflections(R-Free) 5783
    Percent Reflections(Observed) 96.03
    R-Factor(Observed) 0.174
    R-Work 0.1726
    R-Free 0.1999
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.7635
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5505
    Shell Resolution(Low) 1.5681
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 3520
    R-Factor(R-Work) 0.2447
    R-Factor(R-Free) 0.2777
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5681
    Shell Resolution(Low) 1.5865
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3560
    R-Factor(R-Work) 0.2486
    R-Factor(R-Free) 0.3005
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5865
    Shell Resolution(Low) 1.6059
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3618
    R-Factor(R-Work) 0.2576
    R-Factor(R-Free) 0.311
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6059
    Shell Resolution(Low) 1.6262
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3577
    R-Factor(R-Work) 0.2775
    R-Factor(R-Free) 0.3052
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6262
    Shell Resolution(Low) 1.6476
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3578
    R-Factor(R-Work) 0.2301
    R-Factor(R-Free) 0.2595
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6476
    Shell Resolution(Low) 1.6702
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3644
    R-Factor(R-Work) 0.1989
    R-Factor(R-Free) 0.2249
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6702
    Shell Resolution(Low) 1.694
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3568
    R-Factor(R-Work) 0.2029
    R-Factor(R-Free) 0.2278
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.694
    Shell Resolution(Low) 1.7193
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3617
    R-Factor(R-Work) 0.1933
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7193
    Shell Resolution(Low) 1.7462
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 3623
    R-Factor(R-Work) 0.193
    R-Factor(R-Free) 0.2295
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7462
    Shell Resolution(Low) 1.7748
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3579
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2102
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7748
    Shell Resolution(Low) 1.8054
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3631
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.2475
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8054
    Shell Resolution(Low) 1.8382
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3686
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.2214
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8382
    Shell Resolution(Low) 1.8736
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3633
    R-Factor(R-Work) 0.208
    R-Factor(R-Free) 0.2499
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8736
    Shell Resolution(Low) 1.9118
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 3599
    R-Factor(R-Work) 0.2278
    R-Factor(R-Free) 0.2464
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9118
    Shell Resolution(Low) 1.9534
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3631
    R-Factor(R-Work) 0.1918
    R-Factor(R-Free) 0.2377
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9534
    Shell Resolution(Low) 1.9988
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3657
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.2122
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9988
    Shell Resolution(Low) 2.0488
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3694
    R-Factor(R-Work) 0.1704
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0488
    Shell Resolution(Low) 2.1042
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3664
    R-Factor(R-Work) 0.1729
    R-Factor(R-Free) 0.2177
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1042
    Shell Resolution(Low) 2.1661
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 3706
    R-Factor(R-Work) 0.1698
    R-Factor(R-Free) 0.1936
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1661
    Shell Resolution(Low) 2.2361
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3670
    R-Factor(R-Work) 0.1661
    R-Factor(R-Free) 0.1825
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2361
    Shell Resolution(Low) 2.316
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3724
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.2059
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.316
    Shell Resolution(Low) 2.4087
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 3705
    R-Factor(R-Work) 0.1664
    R-Factor(R-Free) 0.2064
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4087
    Shell Resolution(Low) 2.5183
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3738
    R-Factor(R-Work) 0.1754
    R-Factor(R-Free) 0.1875
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5183
    Shell Resolution(Low) 2.651
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3741
    R-Factor(R-Work) 0.1791
    R-Factor(R-Free) 0.2305
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.651
    Shell Resolution(Low) 2.8171
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3744
    R-Factor(R-Work) 0.1758
    R-Factor(R-Free) 0.2282
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8171
    Shell Resolution(Low) 3.0345
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3795
    R-Factor(R-Work) 0.1744
    R-Factor(R-Free) 0.2144
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0345
    Shell Resolution(Low) 3.3398
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 3754
    R-Factor(R-Work) 0.1722
    R-Factor(R-Free) 0.2079
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3398
    Shell Resolution(Low) 3.8227
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3772
    R-Factor(R-Work) 0.1521
    R-Factor(R-Free) 0.1552
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8227
    Shell Resolution(Low) 4.8149
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3766
    R-Factor(R-Work) 0.1333
    R-Factor(R-Free) 0.1448
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8149
    Shell Resolution(Low) 39.7748
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 3720
    R-Factor(R-Work) 0.1642
    R-Factor(R-Free) 0.1885
    Percent Reflections(Observed) 94.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.242
    f_plane_restr 0.005
    f_chiral_restr 0.072
    f_angle_d 1.072
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6284
    Nucleic Acid Atoms 0
    Heterogen Atoms 15
    Solvent Atoms 782
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL