(IUCr) Crystallography Journals Online checkcif report

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Acta Cryst. (2005). E61, o320-o322 [ doi:10.1107/S1600536805000693 ]

[(1-Methylcytosine)₂H]I, an asymmetric base pair

J. Müller and E. Freisinger

Online 22 January 2005

Key indicators

Single-crystal X-ray study
T = 163 K
Mean (C-C) = 0.005 Å
R factor = 0.020
wR factor = 0.043
Data-to-parameter ratio = 13.8

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT035_ALERT_1_A No _chemical_absolute_configuration info given .          ?

Author Response: The presented compound is a racemic twin with twin fractions of 0.52(2) and 0.48(2), thus inversion of the structure yielded identical R values.

PLAT112_ALERT_2_A ADDSYM Detects Additional (Pseudo) Symm. Elem...          n

Author Response: The presented compound features a hemiprotonated cytosine- cytosine base pair with pseudo-centrosymmetry. Solution of the structure in the centrosymmetric space group P21/c with only one cytosine molecule yielded 114 systematic absence violations (62>3s):

    Systematic absence exceptions:
         -21-   -a-   -c-   -n-

  N         5    87    89    88
  N I>3s    0    73    62    75
  <I>     2.6 532.5  56.1 525.0
  <I/s>   0.7  18.1  12.0  18.4

 Refinement in P21/c converged against R1 = 0.0851 for 1192 Fo >
 4sig(Fo) and wR2 =  0.2085 (GooF = 1.484) with N1 and C6 NPD.

PLAT113_ALERT_2_A ADDSYM Suggests Possible Pseudo/New Spacegroup .      P21/c

Author Response: see response above.


Alert level B
PLAT111_ALERT_2_B ADDSYM Detects (Pseudo) Centre of Symmetry .....        100 PerFit

Alert level C
STRVA01_ALERT_4_C           Flack test results are ambiguous.
           From the CIF: _refine_ls_abs_structure_Flack    0.520
           From the CIF: _refine_ls_abs_structure_Flack_su    0.020
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.97       
PLAT033_ALERT_2_C Flack Parameter Value Deviates from Zero .......       0.52       
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT230_ALERT_2_C Hirshfeld Test Diff for    N3     -   C2      ..       5.79 su    
PLAT230_ALERT_2_C Hirshfeld Test Diff for    C5     -   C6      ..       5.37 su    
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          5       
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          1       
              C5 H8 N3 O                                                        

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           25.35
           From the CIF: _reflns_number_total               2519
           Count of symmetry unique reflns         1396
           Completeness (_total/calc)            180.44%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1123
           Fraction of Friedel pairs measured     0.804
           Are heavy atom types Z>Si present        yes

   3 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   8 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   6 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   4 ALERT type 4 Improvement, methodology, query or suggestion

[(1-Methylcytosine)2H]I, an asymmetric base pair

J. Müller and E. Freisinger

Key indicators

checkCIF/PLATON results

[(1-Methylcytosine)₂H]I, an asymmetric base pair