POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4HP4
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 6.5
    Temperature 277.0
    Details 30% PEG5000, 0.35M ammonium sulfate, 0.1M MES, pH 6.5, vapor diffusion, sitting drop, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 150.31 α = 90
    b = 150.31 β = 90
    c = 150.31 γ = 90
     
    Space Group
    Space Group Name:    P 41 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector AREA DETECTOR
    Type ADSC QUANTUM 210
    Collection Date 2009-12-19
     
    Diffraction Radiation
    Diffraction Protocol single wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-1
    Wavelength List 0.933
    Site ESRF
    Beamline ID14-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.6
    Observed Criterion Sigma(I) 1.4
    Resolution(High) 2
    Resolution(Low) 53.15
    Number Reflections(All) 39431
    Number Reflections(Observed) 39431
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.089
    Redundancy 14.7
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.11
    Percent Possible(All) 99.4
    R Merge I(Observed) 0.55
    Mean I Over Sigma(Observed) 1.4
    R-Sym I(Observed) 0.55
    Redundancy 7.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 53.141
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 39360
    Number of Reflections(Observed) 39372
    Number of Reflections(R-Free) 1999
    Percent Reflections(Observed) 99.16
    R-Factor(Observed) 0.1736
    R-Work 0.1727
    R-Free 0.1912
     
    Temperature Factor Modeling
    Mean Isotropic B Value 29.219
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.0504
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2605
    R-Factor(R-Work) 0.2335
    R-Factor(R-Free) 0.259
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0504
    Shell Resolution(Low) 2.1058
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2602
    R-Factor(R-Work) 0.2106
    R-Factor(R-Free) 0.2401
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1058
    Shell Resolution(Low) 2.1678
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2055
    R-Factor(R-Free) 0.2463
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1678
    Shell Resolution(Low) 2.2378
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2619
    R-Factor(R-Work) 0.2074
    R-Factor(R-Free) 0.2498
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2378
    Shell Resolution(Low) 2.3177
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.1808
    R-Factor(R-Free) 0.2271
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3177
    Shell Resolution(Low) 2.4105
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.1766
    R-Factor(R-Free) 0.2004
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4105
    Shell Resolution(Low) 2.5202
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1706
    R-Factor(R-Free) 0.1653
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5202
    Shell Resolution(Low) 2.6531
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.1682
    R-Factor(R-Free) 0.167
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6531
    Shell Resolution(Low) 2.8193
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.1612
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8193
    Shell Resolution(Low) 3.037
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2702
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.1787
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.037
    Shell Resolution(Low) 3.3426
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.1694
    R-Factor(R-Free) 0.1904
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3426
    Shell Resolution(Low) 3.8261
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2707
    R-Factor(R-Work) 0.1545
    R-Factor(R-Free) 0.1812
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8261
    Shell Resolution(Low) 4.82
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2726
    R-Factor(R-Work) 0.1412
    R-Factor(R-Free) 0.1534
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.82
    Shell Resolution(Low) 53.1599
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2792
    R-Factor(R-Work) 0.1943
    R-Factor(R-Free) 0.2115
    Percent Reflections(Observed) 95.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.046
    f_dihedral_angle_d 12.873
    f_angle_d 0.742
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2042
    Nucleic Acid Atoms 0
    Heterogen Atoms 16
    Solvent Atoms 210
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser
    data reduction SCALA version: 3.2.25
    data collection Mosflm