data-precision algorithms

Data-precision indicators are published for all structures reported in Acta Crystallographica Section E. They provide a simple but fair overall assessment of each structure.

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Quality indicator A: R factor

TEST
IF _refine_ls_R_factor_gt > 0.10 score 1.
IF 0.05 < _refine_ls_R_factor_gt > 0.10 score 2.
IF _refine_ls_R_factor_gt < 0.05 score 3.

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Quality indicator B: Data coverage

CALCULATE

S = SIN [_diffrn_reflns_theta_max] / _diffrn_radiation_wavelength

RRRT = _refine_ls_number_reflns / _reflns_number_total

RRTP = _refine_ls_number_reflns / _refine_ls_number_parameters

TEST

IF S < 0.59 OR RRRT < 0.95 THEN PERFORM FOLLOWING TESTS

OTHERWISE score 3.
IF CENTROSYMMETRIC
RRTP < 10 score 2.
RRTP < 6 score 1.

IF NON-CENTROSYMMETRIC
IF ZMAX > 18
RRTP < 10 score 2.
RRTP < 6 score 1.

ELSE
RRTP < 8 score 2.
RRTP < 4 score 1.

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Quality indicator C: Refinement quality

Part 1

PROCEDURE:
TEST
IF |_refine_ls_shift/su_max| < 0.05 score 1.

ELSE score 0.

Part 2

PROCEDURE:
DMAX = _refine_diff_density_max
DTEST = 0.1 * ZMAX

TEST

IF DMAX < 1.0*DTEST score 1. ELSE score 0.

Part 3

Score 1 unless any of the following conditions are met.

PROCEDURE: DEFINE

mu is the value _exptl_absorpt_coefficient_mu
tmax is the distance _exptl_crystal_size_max
tmid is the distance _exptl_crystal_size_mid
tmin is the distance _exptl_crystal_size_min
trad is the radius _exptl_crystal_size_rad

Tmax(rep) is reported _exptl_absorpt_correction_T_max
Tmin(rep) is reported _exptl_absorpt_correction_T_min

TEST

IF _exptl_absorpt_correction_type ~ "psi-scan"
OR "empirical"
OR "multi-scan"
OR "refdelf"

IF mu * tmid > 3.0 score 0.

IF _exptl_absorpt_correction_type is not set as none, but Tmin/Tmax not given, score 0.

 

IF _exptl_absorpt_correction_type ~ "psi-scan"
OR "empirical"
OR "multi-scan"
OR "refdelf"
OR "analytical"
OR "numerical"
OR "gaussian"
OR "none"

CALCULATE

Tmax(shape) = EXP(-tmin * mu)
Tmin(shape) = EXP(-temx * mu)
Tmin(shape)'= EXP(-tmax * mu)

where temx = MAX{tmid, MIN[(1.2*tmid), tmax]}

Tmax(angle) = 1.0
Tmin(angle) = TAB(_diffrn_reflns_theta_max, mu*tmid)
TAB=Lookup value for angular factor

mu*tmid	MoK\a	CuK\a
0.0	1.00	1.00
0.5	1.01	1.05
1.0	1.04	1.15
1.5	1.09	1.25
2.0	1.15	1.5
2.5	1.25	1.9
3.0	1.40	2.5

Tmax(exp) = Tmax(shape) * Tmax(angle)
Tmin(exp) = Tmin(shape) * Tmin(angle)
Tmin(exp)'= Tmin(shape)'/ Tmin(angle)

RT(rep) = Tmax(rep) / Tmin(rep)
RT(exp) = Tmax(exp) / Tmin(exp)
RT(exp)'= Tmax(exp) / Tmin(exp)'

RR = RT(exp) / RT(rep)
RR'= RT(exp)'/ RT(rep)

TEST

IF _exptl_absorpt_correction_type ~ "refdelf"
OR "empirical"
OR "psi-scan"
OR "multi-scan"
THEN
IF RR' < 0.75 OR RR > 1.50 score 0.

ELSE IF _exptl_absorpt_correction_type ~ "none"

THEN
IF RT(exp) > 1.10 score 0.

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Quality indicator D: Order

PROCEDURE:

SUMMATION

(1) For each atomic species in the _chemical_formula_sum string, calculate the number of atoms in the cell using the _chemical_formula_sum counts and the _cell_formula_units_Z.

(2) For each atomic species in the _atom_site_ list, calculate, using the _atom_site_occupancy value and the symmetry site-multiplicity value (generated from NSYM), the number of atoms in the cell.

CALCULATE
For completeness of atom site determination

DN = [cell contents from (1)] - [cell contents from (2)] for each atom type

SUMDN = sum of DN for ALL atom species

For disorder checking

Use PLATON tests _301 and _302

TEST

Score 3. For no reported disorder (main residue and solvent) and all atoms given.

Score 2. If only hydrogens are unaccounted for and/or disorder in solvent and/or < 15% disorder in main residue.

Score 1. For atoms other than hydrogen missing in atom list and/or > 15% disorder in main residue.

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Quality indicator E: Special features

Part 1

PROCEDURE:
TEST
?? score 1.

Part 2

PROCEDURE:

IF structure is centrosymmetric score 1.
OTHERWISE check for absolute structure determination.

FLACK = _refine_ls_abs_structure_flack
SFLACK = su of _refine_ls_abs_structure_flack

TEST if Flack parameter present.
IF FLACK > 0.7 score 0.
ELSE IF FLACK > 0.3 AND FLACK < 0.7 score 0.
ELSE IF FLACK < -0.2 score 0.
ELSE IF SFLACK > 0.5 score 0.

ROGERS = _refine_ls_abs_structure_rogers

TEST if Rogers parameter present.
IF ABS(ROGERS) > 1.2 score 0.
IF ROGERS > -0.5 AND ROGERS < 0.5 score 0.
IF ROGERS < -1.2 score 0
IF ROGERS < -0.5 score 0.
ELSE IF FLACK or ROGERS satisfactory score 1.

IF neither parameter is present score 0.

Part 3

PROCEDURE: (3 parts, score 0 or 1 for each
TEST

IF _cell_measurement_temperature < 273 score 1.
IF _cell_measurement_temperature > 273 score 0.

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