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An atomic basis of a crystal is the motif of chemical species $s_j$ and relative positions $r_j$ attached identically to every lattice point $R$ of a Bravais lattice $\Lambda$. The ideal periodic structure is the labeled setThe primitive lattice translation vectors generate $R$ by integer combinations; the atomic basis lists what is repeated at $R$. These are different meanings of the word basis. In particular, the offsets $r_j$ need not be linearly independent vectors, and one of them may be zero. A primitive unit cell represents $N$ motif sites, even though it represents only one lattice point.

Changing the origin, choosing another primitive unit cell, or moving a motif site by a Bravais lattice translation changes the coordinates used to describe the same infinite crystal structure. The grouping into a motif does not, by itself, identify bonded molecules. In solid sodium chloride, grouping one sodium cation and one chlorine anion into an atomic basis does not create a collection of discrete NaCl molecules; the ionic crystal has an extended network of equivalent neighboring ions.

Beth A. Wilson coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

Bruce E. Bursten coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

Claudia Lewis Randolph coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

The crystal basis structure factor is the coherent sum of scattering contributions from the atomic basis of a crystal at a chosen reciprocal lattice vector $\mathbf{G}$:The positions ${\mathbf{r}}_s$ lie within a cell and $f_s$ are the corresponding scattering amplitudes. Fractional coordinates give $F_{hkl}={\sum }_s{f}_s{e}^{2\pi i(h{x}_s+k{y}_s+l{z}_s)}$.

The Bravais lattice sum fixes possible Bragg-peak positions, while this basis sum controls their amplitudes and can cancel some exactly. Two identical sites separated by half a cubic body diagonal give a factor $1+(-1{)}^{h+k+l}$, extinguishing odd sums. Replacing one site by a different species generally prevents that cancellation. The intensity involves $|F{|}^2$, so amplitudes must be added before squaring.

Crystal isomorphism is a relation between crystal structures that preserves the relevant lattice and structural arrangement while permitting specified atomic replacement or addition. The IUCr definition requires the same space group and unit cell dimensions, with corresponding atom positions and types apart from those substitutions or additions.^[ref] Similar external crystal shapes or equal chemical formulas alone do not establish those conditions.

The relation matters experimentally in single isomorphous replacement and multiple isomorphous replacement. A heavy-atom derivative is useful when the unlabeled parent contribution is sufficiently unchanged to write, in a common coordinate convention,Here $F_P$ is the native structure factor and $F_H$ is the reference contribution from the added heavy atoms. If derivatization also changes the parent structure, a more honest decomposition isThe additional term cannot generally be inferred from the heavy-atom label alone. For original complex amplitudes $F_P=4+3i$ and $F_H=3$, the ideal derivative has squared magnitude58. If a structural change contributes $\Delta F_{\mathrm{structure}}=1$, the squared magnitude becomes73. Interpreting that increase solely as extra label scattering would misattribute the change.

Matching unit-cell dimensions is only one test. An original periodic two-site model illustrates why the atomic basis of a crystal matters too. Put identical point scatterers at fractional coordinates $(0,0,0)$ and $(1/2,0,0)$. For the $(100)$ reflection their amplitudes cancel. Moving the second site to $(1/2+\delta ,0,0)$ without changing the cell dimensions giveswhere $f$ is the common atomic scattering factor. At $\delta =0.01$, the magnitude is about $0.0628|f|$ rather than zero. The stipulated model is not an experimental derivative; it shows how unchanged lattice spacing can coexist with changed diffraction intensities from shifted atoms.

In actual phasing, crystal isomorphism is an approximation to assess across the measured X-ray diffraction data. The ideal vector-circle constructions assume comparable native and derivative amplitudes and consistently referenced heavy-atom positions.^[ref] Preserved cell metrics support that comparison, but cannot by themselves prove the unchanged-parent assumption.

Crystallographic symmetry consists of the spatial transformations that leave an ideal crystal structure unchanged, including the identities of its chemical atoms. A symmetry of the crystal lattice alone need not preserve the atomic basis of a crystal. The full set of crystal-preserving transformations forms a space group; its translational part distinguishes it from a crystallographic point symmetry description.^[ref]

In fractional unit cell coordinates a space group operation has the form $x\mapsto Wx+w$. The matrix $W$ describes its linear action and $w$ its translation. A screw axis combines a rotation with a translation parallel to the axis; a glide plane combines reflection with translation within the plane. For example, a twofold screw can act asApplying it twice gives $(x,y,z+1)$, a full unit cell translation. Replacing it by a pure twofold rotation would lose this relation between orientation and position.

For ordinary three-dimensional periodic crystals, the possibilities are organized into 32 crystallographic point groups and 230 space groups. These counts concern spatial symmetry without additional magnetic labels. A square outline alone does not establish fourfold symmetry: decorating alternate corners with different atoms can break the rotation. In structure determination, the symmetry therefore constrains both the lattice geometry and which sites can carry equivalent chemical atoms.^[ref]

Crystallography studies crystal structures and their symmetries. A structure determination connects measurements such as crystal scattering patterns to a model of the unit cell and its atomic basis of a crystal.

X-ray crystallographic structure inference makes that connection explicit: compare proposed crystal structures through the positions and wave intensities of their predicted reflections. The main difficulty is that a diffraction pattern encodes wave interference, so it must be interpreted through a model rather than read as a direct picture of the chemical atoms.

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

For a concrete two-dimensional model, choose primitive lattice translation vectors $a_1=(2,0)$ and $a_2=(0,1.5)$ in arbitrary length units. At every lattice point $R=m{a}_1+n{a}_2$, with integers $m,n$, place species A at $R$ and a different species B at $R+(0.65,0.55)$. Translating by $a_1$ or $a_2$ preserves both the positions and their chemical labels. Translating by $(0.65,0.55)$ sends one A position to a B position, so it is not a translation symmetry of the labeled structure. A picture of dots with the labels erased can therefore conceal essential chemical information.

A primitive unit cell contains one lattice point, but may contain several chemical atoms. A conventional unit cell can contain several lattice points to display the symmetry more clearly. Thus the conventional cube of a face-centered cubic lattice contains four lattice points, whereas a body-centered cubic lattice has two. Neither lattice name alone specifies which chemical species occupies the repeated motif. The NaCl conventional cell and coordination example makes the distinction explicit.

This separation is useful experimentally: interplanar spacings constrain the repeating geometry, while relative wave intensities also depend on the atomic basis of a crystal through the crystal basis structure factor. The Bragg crystal reflection experiment of 1913 describes the X-ray spectrometer, angular scans and detector checks in detail. Its conversion from angle to length is developed under Bragg's law; a geometrically possible reflection can still have zero wave intensity.

William Lawrence Bragg's 1913 structure determination supplied a complementary test. He directed X-rays through sodium chloride sections cut parallel to a cube face and recorded spots on photographic plates. Comparing section thicknesses tested how transmission altered the pattern: the relative spot strengths changed. Comparing related salts led him to two interpenetrating face-centered cubic lattices, one for each kind of constituent. He explicitly distinguished evidence for that arrangement from the still-needed identification of a single chemical atom with each scattering center. The photographs were evidence for a structural model, not direct pictures of labeled ions.^[ref]

For equivalent scatterers on the four conventional fcc sites, the centering factor is $1+e^{i\pi (h+k)}+e^{i\pi (h+l)}+e^{i\pi (k+l)}$. It is four when the integer indices are all even or all odd, and zero otherwise. An additional atomic basis of a crystal can impose further extinctions. This rule concerns conventional cubic indexing.

John C. Dewan coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

John C. Huffman coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

John G. Kester coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

John L. Little coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

Josephine Paw Blaha coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

Karolin Luger coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

Lee J. Todd coauthored research on crystal structure.^[ref]

A crystal structure specifies the chemical species and spatial arrangement of the chemical atoms or ions in a crystal. For an ideal periodic structure, separate two ingredients: a Bravais lattice specifies the translations that repeat the arrangement, and an atomic basis of a crystal specifies the chemical motif repeated at every lattice point. The outward shape, or crystal habit, is a different description: the internal arrangement is what this article describes.

Use the total scattering angle $\psi =2\theta$. For a cubic unit cell, Bragg's law and the Miller indices giveThe four measured values of ${\sin }^2\theta$, normalized to the first, are $1,1.330,2.655,3.649$. Multiplying by three gives approximately $3,4,8,11$, the initial allowed sequence for a face-centered cubic lattice:The FCC lattice factor is $1+(-1{)}^{h+k}+(-1{)}^{h+l}+(-1{)}^{k+l}$; it vanishes unless all three indices have the same parity. Thus the initial ratios differ from those of a primitive or body-centered cubic lattice. This is the conventional minimal cubic indexing; arbitrarily hiding additional weak reflections could make a short list alone ambiguous.

The low-pressure rock salt structure has an FCC Bravais lattice with one NaCl formula unit per primitive unit cell, or four per conventional cube. A possible atomic basis of a crystal is Na at zero and Cl at $(1/2,0,0)$ in conventional fractional coordinates. The two species have unequal atomic scattering factors, so both the odd and even FCC families can occur.

The four independent lattice constant estimates areTheir small scatter reflects the rounded angular data. The appropriate reported result is

The high-pressure atomic basis of a crystal has the caesium chloride structure. Its chemically labelled Bravais lattice is simple cubic lattice: exchanging Na and Cl is not a translation symmetry. Its structure factor isBecause ionic bonding gives approximately Na${}^{+}$ and Cl${}^{-}$, their bound-electron counts are $10$ and $18$. In the stipulated electron-count approximation, odd-index-sum reflections have $|F|=8$, while even-index-sum reflections have $|F|=28$. In particular, the first ring $\{100\}$ is weak but present; it must not be discarded using a body-centering extinction rule.

The next ring is $\{110\}$, and Bragg's law givesThe powder diffraction multiplicities are six and twelve. Counting all symmetry-equivalent reflections, while neglecting other angular factors, therefore givesThe corresponding single-directed-reflection ratio would be $12.25$. Neutral-atom counts would give the wrong contrast because the material is ionic.

For measured integrated photon counts, the geometry must also be specified. More generally the ratio is $2|F_{110}/F_{100}{|}^2$ times the ratio of Lorentz-polarization factors, thermal-motion factors and detection efficiencies. For example, the common unpolarized symmetric-powder convention hasand gives $24.5LP(21.2506^{\circ })/LP(14.85^{\circ })\simeq 11.18$ if all other corrections are suppressed. Thus 24.5 is the multiplicity-and-structure-factor estimate, rather than a geometry-independent precision count ratio; actual angle-dependent ionic form factors are also not supplied.

The sites form a face-centered cubic lattice decorated by an identical two-atom atomic basis of a crystal, at fractional displacements $0$ and $\mathbf{\delta }=(1/4,1/4,1/4)$. This is the diamond cubic structure; the eight atoms in its conventional cube are not eight independent Bravais-lattice points.

For identical silicon atomic scattering factors $f$, the conventional-cell structure factor separates into the FCC factor and the two-site motif factor:The first factor vanishes unless $h,k,l$ are all even or all odd. For all-even indices, the motif also vanishes if $h+k+l=4r+2$; it survives if the sum is divisible by four. All-odd indices survive, with motif modulus $\sqrt{2}$. Thus $(100)$ and $(110)$ are absent by centering, $(200)$ is absent by the diamond basis, and $(111)$ and $(220)$ are allowed.

For a cubic cell, $d_{hkl}=a/\sqrt{h^2+k^2+l^2}$. At fixed X-ray wavelength, Bragg's law makes the smallest scattering angles correspond to the smallest allowed positive values of $h^2+k^2+l^2$. These start with $3$ and $8$, soThe braces denote whole powder families, including their symmetry-equivalent plane normals. The next family is $\{311\}$, with squared-index sum $11$; using the FCC rule alone would incorrectly insert a $(200)$ line before $(220)$.