This section describes the geometry of the crystallographic experiment and the coordinate system transformations.
Overview
The CRYST1 record presents the unit cell parameters, space group, and Z value. If the structure was not determined by crystallographic means, CRYST1 simply provides the unitary values, with an appropriate REMARK.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------- 1 - 6 Record name "CRYST1" 7 - 15 Real(9.3) a a (Angstroms). 16 - 24 Real(9.3) b b (Angstroms). 25 - 33 Real(9.3) c c (Angstroms). 34 - 40 Real(7.2) alpha alpha (degrees). 41 - 47 Real(7.2) beta beta (degrees). 48 - 54 Real(7.2) gamma gamma (degrees). 56 - 66 LString sGroup Space group. 67 - 70 Integer z Z value.
Details
As an example, given two chains A and B, each with a different sequence, and the space group P 2 that has two equipoints in the standard unit cell, the following table gives the correct Z value.
Asymmetric Unit Content Z value
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A 2
AA 4
AB 2
AAB 4
AABB 4
Verification/Validation/Value Authority Control
The given space group and Z values are checked during processing for correctness and internal consistency. The calculated SCALE factor is compared to that supplied by the depositor. Packing is also computed, and close contacts of symmetry-related molecules are diagnosed.
Relationships to Other Record Types
The unit cell parameters are used to calculate SCALE. If the EXPDTA record is NMR, Electron microscopy, or Fiber Diffraction, the CRYST1 record is predefined as in the last example (see below). In these cases, an explanatory REMARK must also appear in the entry. Some fiber diffraction structures will be done this way, while others will have a CRYST1 record containing measured values.
Examples
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
CRYST1 52.000 58.600 61.900 90.00 90.00 90.00 P 21 21 21 8
CRYST1 42.544 69.085 50.950 90.00 95.55 90.00 P 1 21 1 2
Example of experimental method other than X-ray crystallography or fiber diffraction
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
Known Problems
No standard deviations are given.
Overview
The ORIGXn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------- 1 - 6 Record name "ORIGXn" n=1, 2, or 3 11 - 20 Real(10.6) o[n][1] On1 21 - 30 Real(10.6) o[n][2] On2 31 - 40 Real(10.6) o[n][3] On3 46 - 55 Real(10.5) t[n] Tn
Details
Xsub = O11X + O12Y + O13Z + T1 Ysub = O21X + O22Y + O23Z + T2 Zsub = O31X + O32Y + O33Z + T3
Verification/Validation/Value Authority Control
If the coordinates are submitted in the same orthogonal Angstrom coordinate frame as they appear in the entry (the usual case), then ORIGX is an identity matrix with a null translation vector. If the transformation is not an identity matrix with a null translation vector, then applying this transformation to the coordinates in the entry yields the coordinates of the original deposited file.
Relationships to Other Record Types
ORIGX relates the coordinates in the ATOM and HETATM records to the coordinates in the file.
Example
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 ORIGX1 0.963457 0.136613 0.230424 16.61000 ORIGX2 -0.158977 0.983924 0.081383 13.72000 ORIGX3 -0.215598 -0.115048 0.969683 37.65000
Overview
The SCALEn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates as contained in the entry to fractional crystallographic coordinates. Non-standard coordinate systems should be explained in the remarks.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------ 1 - 6 Record name "SCALEn" n=1, 2, or 3 11 - 20 Real(10.6) s[n][1] Sn1 21 - 30 Real(10.6) s[n][2] Sn2 31 - 40 Real(10.6) s[n][3] Sn3 46 - 55 Real(10.5) u[n] Un
Details
If vector a, vector b, vector c describe the crystallographic cell edges, and vector A, vector B, vector C are unit cell vectors in the default orthogonal Angstroms system, then vector A, vector B, vector C and vector a, vector b, vector c have the same origin; vector A is parallel to vector a, vector B is parallel to vector C times vector A, and vector C is parallel to vector a times vector b (i.e., vector c*). * If the orthogonal Angstroms coordinates are X, Y, Z, and the fractional cell coordinates are xfrac, yfrac, zfrac, then:
xfrac = S11X + S12Y + S13Z + U1
yfrac = S21X + S22Y + S23Z + U2
zfrac = S31X + S32Y + S33Z + U3
Verification/Validation/Value Authority Control
The inverse of the determinant of the SCALE matrix equals the volume of the cell. This volume is calculated and compared to the SCALE matrix supplied by the depositor.
Relationships to Other Record Types
The SCALE transformation is related to the CRYST1 record, as the inverse of the determinant of the SCALE matrix equals the cell volume.
Example
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SCALE1 0.019231 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017065 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016155 0.00000
Overview
The MTRIXn (n = 1, 2, or 3) records present transformations expressing non-crystallographic symmetry. MTRIXn will appear only when such transformations are required to generate an entire asymmetric unit, such as a large viral structure.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------- 1 - 6 Record name "MTRIXn" n=1, 2, or 3 8 - 10 Integer serial Serial number. 11 - 20 Real(10.6) m[n][1] Mn1 21 - 30 Real(10.6) m[n][2] Mn2 31 - 40 Real(10.6) m[n][3] Mn3 46 - 55 Real(10.5) v[n] Vn 60 Integer iGiven 1 if coordinates for the representations which are approximately related by the transformations of the molecule are contained in the entry. Otherwise, blank.
Details
Verification/Validation/Value Authority Control
All MTRIX records are verified using records from the author and review.
Relationships to Other Record Types
None.
Example
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
MTRIX1 1 -1.000000 0.000000 0.000000 0.00000 1
MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1
MTRIX3 1 0.000000 0.000000 -1.000000 0.00000 1