POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VA5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 277.0
    Details 20% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 31.18 α = 90
    b = 60.27 β = 94.78
    c = 38.1 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type PSI PILATUS 6M
    Collection Date 2011-09-25
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 0.97950
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.55
    Resolution(Low) 50
    Number Reflections(All) 20327
    Number Reflections(Observed) 20327
    Percent Possible(Observed) 98.2
    R Merge I(Observed) 0.066
    B(Isotropic) From Wilson Plot 32.3
    Redundancy 5.8
     
    High Resolution Shell Details
    Resolution(High) 1.55
    Resolution(Low) 1.58
    Percent Possible(All) 85.9
    R Merge I(Observed) 0.336
    Mean I Over Sigma(Observed) 3.5
    Redundancy 4.2
    Number Unique Reflections(All) 865
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.55
    Resolution(Low) 32.12
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 20146
    Number of Reflections(Observed) 20146
    Number of Reflections(R-Free) 2046
    Percent Reflections(Observed) 98.59
    R-Factor(All) 0.1793
    R-Factor(Observed) 0.1793
    R-Work 0.1751
    R-Free 0.2185
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.3955
    Anisotropic B[1][1] -1.57
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.01
    Anisotropic B[2][2] -1.01
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.75
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.55
    Shell Resolution(Low) 1.59
    Number of Reflections(Observed) 1346
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1208
    R-Factor(R-Work) 0.311
    R-Factor(R-Free) 0.285
    Percent Reflections(Observed) 89.97
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.917
    r_scbond_it 3.222
    r_mcangle_it 2.163
    r_mcbond_it 1.459
    r_gen_planes_refined 0.016
    r_chiral_restr 0.162
    r_dihedral_angle_4_deg 10.054
    r_dihedral_angle_3_deg 14.577
    r_dihedral_angle_2_deg 33.985
    r_dihedral_angle_1_deg 6.134
    r_angle_refined_deg 1.719
    r_bond_refined_d 0.017
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1028
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 111
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0110
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser version: 2.2.1
    data reduction SCALEPACK