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Crystallography terms

Mary S 12 questions

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  1. 1What makes good data?
    1. [blank_start]Rmerge[blank_end] = [blank_start]lower[blank_end] the better. This is how much [blank_start]measurements of the same reflection[blank_end] differ from the [blank_start]average intensity[blank_end] of [blank_start]that reflection[blank_end].
    Rmeas = same as R merge but [blank_start]independent[blank_end] of [blank_start]multiplicity[blank_end].

    2. I/sigma I = Signal to [blank_start]noise[blank_end] ratio. [blank_start]>2[blank_end] good, [blank_start]>1[blank_end] okay. [blank_start]Completeness[blank_end] = reports on missing data, aim for [blank_start]100[blank_end] %.

    Multiplicity = aim [blank_start]high[blank_end] [blank_start]> 3[blank_end]. No of [blank_start]unique reflections[blank_end].
    CC1/2 = [blank_start]close to 1[blank_end]. Correlation coefficient. If cc1/2 < 0.15, data is insignificant.
    1. ARmerge
    2. Blower
    3. Cmeasurements of the same reflection
    4. Daverage intensity
    5. Ethat reflection
    6. Findependent
    7. Gmultiplicity
    8. Hnoise
    9. I>2
    10. J>1
    11. KCompleteness
    12. L100
    13. Mhigh
    14. N> 3
    15. Ounique reflections
    16. Pclose to 1
  2. 2R [blank_start]work[blank_end] = measure of [blank_start]model errors[blank_end]/ relative [blank_start]discrepancy[blank_end] between [blank_start]experimentally[blank_end] observed structure factor [blank_start]amplitudes[blank_end] ([blank_start]Fhkl[blank_end]) and the ones calculated from the [blank_start]model[blank_end] ([blank_start]Fcalc[blank_end]).

    Combines error from experimental data + deviation of model from reality.
    1. Awork
    2. Bmodel errors
    3. Cdiscrepancy
    4. Dexperimentally
    5. Eamplitudes
    6. FFhkl
    7. Gmodel
    8. HFcalc
  3. 3R [blank_start]free[blank_end] = calculated like R work BU only uses approx [blank_start]1000 randomly selected reflections[blank_end] which never entered model [blank_start]refinement[blank_end]. It can highlight [blank_start]overfitting[blank_end] of data. It should be within [blank_start]7-10[blank_end] % of R work.
    1. Afree
    2. B1000 randomly selected reflections
    3. Crefinement
    4. Doverfitting
    5. E7-10
  4. 43 factors that dictate how diffracted X rays combine to form an image.
    1. [blank_start]Direction[blank_end] - given by [blank_start]Miller indices[blank_end] of [blank_start]crystal plane[blank_end]
    2. [blank_start]Amplitude[blank_end] - from [blank_start]measured intensity[blank_end] of the [blank_start]beam[blank_end]
    3. Phase - [blank_start]no way[blank_end] to observe aka phase problem
    Uses calculations to give str factors from approx arrangement of all or some atoms.
    1. ADirection
    2. BMiller indices
    3. Ccrystal plane
    4. Dmeasured intensity
    5. Ebeam
    6. Fno way
    7. GAmplitude
  5. 5Resolution = [blank_start]minimum[blank_end] [blank_start]spacing[blank_end] of crystal [blank_start]lattice planes[blank_end] that still give measurable [blank_start]diffraction[blank_end] of X-rays.
    The smaller d is, the more [blank_start]independent[blank_end] reflections are [blank_start]available[blank_end] to [blank_start]define[blank_end] the structure.
    1. Aminimum
    2. Bspacing
    3. Clattice planes
    4. Ddiffraction
    5. Eindependent
    6. Favailable
    7. Gdefine
  6. 6Space group = Describes a cell's [blank_start]internal symmetry[blank_end] elements.
    1. Ainternal symmetry
  7. 7[blank_start]Unit cell[blank_end] = smallest and simplest [blank_start]volume element[blank_end] that completely represents the [blank_start]whole crystal[blank_end].
    1. Avolume element
    2. Bwhole crystal
    3. CUnit cell
  8. 8Ramachandran plot = a space filling model of peptides used to [blank_start]visualise energetically possible[blank_end] and [blank_start]sterically permitted[blank_end] values of [blank_start]dihedral angles[blank_end] of polypeptide.
    Shows [blank_start]statistical distribution[blank_end] of the [blank_start]combinations of backbone dihedral[blank_end] angles.

    The allowed regions show which values of [blank_start]phi/psi angles[blank_end] are possible per aa.
    1. Avisualise energetically possible
    2. Bsterically permitted
    3. Cdihedral angles
    4. Dstatistical distribution
    5. Ecombinations of backbone dihedral
    6. Fphi/psi angles
  9. 9Friedel pair - equal [blank_start]amplitude[blank_end], opposite [blank_start]phase[blank_end]. [blank_start]Fhkl[blank_end].
    1. AFhkl
    2. Bamplitude
    3. Cphase
  10. 10[blank_start]CC 1/2[blank_end] = Pearson's correlation coefficient. Based on random division of [blank_start]complete[blank_end] set of [blank_start]reflections[blank_end] into 2 [blank_start]equal[blank_end] parts and calculating [blank_start]correlation[blank_end] between the [blank_start]intensity[blank_end] estimates of the 2. aka how well one half of the data [blank_start]predicts the other half[blank_end].
    1. ACC 1/2
    2. Bcomplete
    3. Creflections
    4. Dequal
    5. Ecorrelation
    6. Fintensity
    7. Gpredicts the other half

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Description
Science Quiz on Crystallography terms, created by Mary S on 30/05/2024.
Author
Mary S
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English
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