Metallohelices that kill Gram-negative pathogens using intracellular antimicrobial peptide pathways
Simpson, Daniel; Hapeshi, Alexia; Rogers, Nicola J.; Brabec, Viktor; Clarkson, Guy J.; Fox, David; Hrabina, Ondrej; Kay, Gemma; King, Andrew; Malina, Jaroslav; Millard, Andrew; Moat, John; Roper, David I.; Song, Hualong; Waterfield, Nick; Scott, Peter; Chemical Science  (2019) –; doi:10.1039/C9SC03532J

data_1552284
_publ_section_title
;
 Metallohelices that kill Gram-negative pathogens using intracellular
 antimicrobial peptide pathways
;
_journal_name_full               'Chemical Science'
_journal_paper_doi               10.1039/C9SC03532J
_journal_year                    2019
_chemical_absolute_configuration rm
_chemical_formula_moiety         'C108 H102 N12 O6 Zn2, 4(Cl O4), 2(C2 H3 N)'
_chemical_formula_sum            'C112 H108 Cl4 N14 O22 Zn2'
_chemical_formula_weight         2274.66
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2018-12-15
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3510 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2019-03-21 deposited with the CCDC.    2019-09-04 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 117.839(3)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   12.3149(4)
_cell_length_b                   40.4691(4)
_cell_length_c                   12.3281(2)
_cell_measurement_reflns_used    10930
_cell_measurement_temperature    150(2)
_cell_measurement_theta_max      76.0640
_cell_measurement_theta_min      4.1870
_cell_volume                     5432.9(3)
_computing_cell_refinement       'CrysAlisPro 1.171.38.43d (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.43d (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.43d (Rigaku OD, 2015)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_diffrn_ambient_temperature      150(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.2833
_diffrn_detector_type            Ruby
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.977
_diffrn_measurement_details
'List of Runs (angles in degrees, time in seconds): # Type Start End Width t~exp~ \w \q \k \f Frames -------------------------------------------------------------------------- 1 \w -4.00 21.00 0.50 13.00 -- 0.00 -99.00-180.00 50 2 \w -3.00 41.00 0.50 13.00 -- 0.00 -99.00 -90.00 88 3 \w -90.00 -40.00 0.50 13.00 -- 0.00-178.00-120.00 100 4 \w -29.00 111.00 0.50 52.00 -- 59.16 -15.00-180.00 280 5 \w 97.00 123.00 0.50 52.00 -- 59.16 122.00-171.00 52 6 \w 105.00 130.00 0.50 52.00 -- 59.16 125.00 90.00 50 7 \w 103.00 147.00 0.50 52.00 -- 59.16 125.00 150.00 88 8 \w -45.00 -19.00 0.50 52.00 -- -73.50 38.00 -90.00 52 9 \w 35.00 83.00 0.50 52.00 -- 118.33 -25.00 -30.00 96 10 \w 28.00 94.00 0.50 52.00 -- 118.33 -25.00-120.00 132 11 \w 37.00 90.00 0.50 52.00 -- 118.33 -25.00-180.00 106 12 \w 40.00 101.00 0.50 52.00 -- 118.33 -50.00 0.00 122 13 \w 107.00 133.00 0.50 52.00 -- 118.33 122.00-171.00 52 14 \w 77.00 178.00 0.50 52.00 -- 118.33 77.00-120.00 202 15 \w 77.00 178.00 0.50 52.00 -- 118.33 77.00 -90.00 202'
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Xcalibur, Ruby, Gemini'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0373674000
_diffrn_orient_matrix_UB_12      -0.0318965000
_diffrn_orient_matrix_UB_13      0.0770659000
_diffrn_orient_matrix_UB_21      0.0337627000
_diffrn_orient_matrix_UB_22      0.0204124000
_diffrn_orient_matrix_UB_23      0.1169243000
_diffrn_orient_matrix_UB_31      -0.1322128000
_diffrn_orient_matrix_UB_32      -0.0038354000
_diffrn_orient_matrix_UB_33      -0.0189521000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0220
_diffrn_reflns_av_unetI/netI     0.0407
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.977
_diffrn_reflns_limit_h_max       13
_diffrn_reflns_limit_h_min       -7
_diffrn_reflns_limit_k_max       49
_diffrn_reflns_limit_k_min       -50
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            20417
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.964
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         76.772
_diffrn_reflns_theta_min         3.276
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.091
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.10594
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'CrysAlisPro 1.171.38.43d (Rigaku Oxford Diffraction, 2015) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.'
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.390
_exptl_crystal_description       block
_exptl_crystal_F_000             2364
_exptl_crystal_size_max          0.124
_exptl_crystal_size_mid          0.116
_exptl_crystal_size_min          0.074
_refine_diff_density_max         0.410
_refine_diff_density_min         -0.345
_refine_diff_density_rms         0.050
_refine_ls_abs_structure_details
;
 Flack x determined using 4872 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.016(11)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.023
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1615
_refine_ls_number_reflns         15808
_refine_ls_number_restraints     432
_refine_ls_restrained_S_all      1.064
_refine_ls_R_factor_all          0.0489
_refine_ls_R_factor_gt           0.0464
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0854P)^2^+0.6202P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1248
_refine_ls_wR_factor_ref         0.1276
_reflns_Friedel_coverage         0.946
_reflns_Friedel_fraction_full    0.994
_reflns_Friedel_fraction_max     0.951
_reflns_number_gt                14918
_reflns_number_total             15808
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c9sc03532j3.cif
_cod_data_source_block           ak2z
_cod_original_cell_volume        5432.9(2)
_cod_database_code               1552284
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         'C120 H120 N14 O21 Cl4 Zn2'
_reflns_odcompleteness_completeness 79.63
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     69.95
_olex2_refinement_description
;
The asymmetric unit contains the Zn helix, four ClO4 counter ions and two molecules of acetonitrile. 
Twice all this in the unit cell. 

The data suffers from being weak and recorded in the higher symmetry orthorhombic cell. 
Mistakenly choose a collection strategy based on the purported higher 
symmetry C centred cell which had a very low Figure of Merit and R(symm).
Only once the structure was finally solved in the lower symmetry monoclinic cell
of half the volume was the mistake realised by which time it was not possible 
to regrow the crystals. 
This does not effect the structure determination but will mean a lower Friedel pair coverage. 
Fortunately the synthesis is from an amino alcohol of known chirality giving unequivocal 
assignment of the handedness of the crystal structure. More details below.

Twinning
All crystals investigated had some problems. Data from the best diffracting sample is reported here.
The structure is twinned about the b axis swapping the a and c axis. The twin components refine to 0.5276(14).
The twinning is about a two fold axis so does not effect the homochirality of the sample.
  
The Flack parameter as a measure of the confidence you can have in assignment of the handedness of the 
crystal chosen is Flack x: -0.016(11) [Hooft y: -0.016(9)] 
This is relatively low with a lowish error but the wrong collection strategy means there is low number of 
Friedel pairs recorded. 
Fortunately, the synthesis has been conducted from an aminoalcohol molecule of known chirality.

Disorder modelling.
There was a lot of disorder in the structure.

The occupancy of the disordered components was originally linked to free variables but once they had settled 
these were fixed at set values at the latter stages of the refinement.

Two of the bridging bis m-xylene ethers were modeled as disordered over two positions.
The disorder of the m-xylyl group was traced all the way between the two ether oxygens O3 to O4.
Xylyl group C51 to C58 was modeled as disordered over two positions related by a small shift. 
The occupancy of the two components was fixed at 60:40. 
Xylyl  C87 to C94 was also modeled over two positions. 
The disorder of the xylyl group was traced all the way between the two ether oxygens O5 to O6.
The occupancy of the two components was fixed at 50 percent occupancy. 
Perchlorates Cl30- O34 and Cl40-O44 where modeled over two positions related by a small shift in the anion.
The occupancy of the two components of Cl30/Cl3A was fixed at 60:40.
The occupancy of the two components of Cl40/Cl4A was fixed at 50:50.
All atoms were refined anisotropically.
Several DFIX, DANG and SIMU restraints were used to give the disordered components reasonably 
bond lengths, angles and thermal parameters.

1. Twinned data refinement
 Scales: 0.4724(14)
 0.5276(14)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
3. Restrained distances
 Cl30-O31 = Cl30-O32 = Cl30-O33 = Cl30-O34
 1.414 with sigma of 0.02
 O31-O32 = O31-O33 = O31-O34 = O32-O33 = O32-O34 = O33-O34
 2.309 with sigma of 0.02
 Cl3A-O31A = Cl3A-O32A = Cl3A-O33A = Cl3A-O34A
 1.414 with sigma of 0.02
 O31A-O32A = O31A-O33A = O31A-O34A = O32A-O33A = O32A-O34A = O33A-O34A
 2.309 with sigma of 0.02
 Cl4A-O41A = Cl4A-O42A = Cl4A-O43A = Cl4A-O44A
 1.414 with sigma of 0.02
 O41A-O42A = O41A-O43A = O41A-O44A = O42A-O43A = O42A-O44A = O43A-O44A
 2.309 with sigma of 0.02
 Cl40-O41 = Cl40-O42 = Cl40-O43 = Cl40-O44
 1.414 with sigma of 0.02
 O41-O42 = O41-O43 = O41-O44 = O42-O43 = O42-O44 = O43-O44
 2.309 with sigma of 0.02
 H103-H95D
 -1.95 with sigma of 0.02
4. Uiso/Uaniso restraints and constraints
Cl10 \\sim O12 \\sim O11 \\sim O13 \\sim O14: within 1.7A with sigma of 0.004
and sigma for terminal atoms of 0.008
Cl20 \\sim O22 \\sim O21 \\sim O23 \\sim O24: within 1.7A with sigma of 0.004
and sigma for terminal atoms of 0.008
Cl30 \\sim O32 \\sim O31 \\sim O33 \\sim O34: within 1.7A with sigma of 0.004
and sigma for terminal atoms of 0.008
N12 \\sim N11 \\sim C104 \\sim C108 \\sim C105 \\sim C106 \\sim C103 \\sim
C107: within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02
Cl3A \\sim O33A \\sim O31A \\sim O32A \\sim O34A: within 1.7A with sigma of
0.01 and sigma for terminal atoms of 0.02
O5 \\sim O6A \\sim C87A \\sim O6 \\sim C88A \\sim C93A \\sim C92A \\sim C91A
\\sim C90A \\sim C89A: within 1.7A with sigma of 0.01 and sigma for terminal
atoms of 0.02
Cl40 \\sim O42 \\sim O44 \\sim O43 \\sim O41 \\sim Cl4A \\sim O41A \\sim O42A
\\sim O43A \\sim O44A: within 1.7A with sigma of 0.004 and sigma for terminal
atoms of 0.008
O3A \\sim C51A \\sim C52A \\sim C53A \\sim C54A \\sim C55A \\sim C56A \\sim
C57A \\sim C58A: within 1.7A with sigma of 0.02 and sigma for terminal atoms of
0.04
5. Others
 Fixed Sof: Cl40(0.5) Cl30(0.6) C52(0.6) C56(0.6) C95A(0.5) H95A(0.5)
 H95B(0.5) O34(0.6) O33(0.6) O31(0.6) H50A(0.6) H50B(0.6) H50C(0.4) H50D(0.4)
 O3(0.6) O6A(0.5) C94A(0.5) H94A(0.5) H94B(0.5) C53(0.6) H53(0.6) C54(0.6)
 H54(0.6) C57(0.6) H57(0.6) H96(0.5) H96A(0.5) C55(0.6) H55(0.6) C51(0.6)
 H51A(0.6) H51B(0.6) O42(0.5) C95(0.5) H95C(0.5) H95D(0.5) O44(0.5) O43(0.5)
 C87A(0.5) H87A(0.5) H87B(0.5) O6(0.5) C94(0.5) H94C(0.5) H94D(0.5) O32(0.6)
 C58(0.6) H58A(0.6) H58B(0.6) C88A(0.5) C93A(0.5) H93A(0.5) C92A(0.5) C91A(0.5)
 H91A(0.5) C90A(0.5) H90A(0.5) C89A(0.5) H89A(0.5) C88(0.5) C93(0.5) H93(0.5)
 C92(0.5) C91(0.5) H91(0.5) C90(0.5) H90(0.5) C89(0.5) H89(0.5) O41(0.5)
 Cl3A(0.4) Cl4A(0.5) O41A(0.5) O42A(0.5) O33A(0.4) O31A(0.4) C87(0.5) H87C(0.5)
 H87D(0.5) O32A(0.4) O43A(0.5) O44A(0.5) O3A(0.4) C51A(0.4) H51C(0.4) H51D(0.4)
 C52A(0.4) C53A(0.4) H53A(0.4) C54A(0.4) H54A(0.4) C55A(0.4) H55A(0.4)
 C56A(0.4) C57A(0.4) H57A(0.4) C58A(0.4) H58C(0.4) H58D(0.4) O34A(0.4)
6.a Ternary CH refined with riding coordinates:
 C60(H60), C79(H79), C43(H43), C24(H24), C7(H7), C96(H96), C96(H96A)
6.b Secondary CH2 refined with riding coordinates:
 C23(H23A,H23B), C95A(H95A,H95B), C50(H50A,H50B), C50(H50C,H50D), C86(H86A,
 H86B), C94A(H94A,H94B), C15(H15A,H15B), C59(H59A,H59B), C51(H51A,H51B),
 C14(H14A,H14B), C95(H95C,H95D), C87A(H87A,H87B), C22(H22A,H22B), C94(H94C,
 H94D), C58(H58A,H58B), C87(H87C,H87D), C51A(H51C,H51D), C58A(H58C,H58D)
6.c Aromatic/amide H refined with riding coordinates:
 C102(H102), C35(H35), C84(H84), C26(H26), C4(H4), C47(H47), C10(H10), C6(H6),
 C74(H74), C82(H82), C48(H48), C19(H19), C72(H72), C78(H78), C66(H66), C30(H30),
  C38(H38), C81(H81), C67(H67), C17(H17), C1(H1), C34(H34), C76(H76), C62(H62),
 C49(H49), C29(H29), C101(H101), C39(H39), C99(H99), C33(H33), C71(H71),
 C108(H108), C45(H45), C9(H9), C75(H75), C37(H37), C27(H27), C42(H42), C12(H12),
  C65(H65), C36(H36), C69(H69), C98(H98), C73(H73), C21(H21), C64(H64),
 C105(H105), C13(H13), C2(H2), C46(H46), C100(H100), C31(H31), C53(H53),
 C54(H54), C57(H57), C63(H63), C40(H40), C18(H18), C55(H55), C85(H85),
 C106(H106), C103(H103), C28(H28), C70(H70), C83(H83), C11(H11), C3(H3),
 C107(H107), C93A(H93A), C91A(H91A), C90A(H90A), C89A(H89A), C93(H93), C91(H91),
  C90(H90), C89(H89), C53A(H53A), C54A(H54A), C55A(H55A), C57A(H57A)
6.d Fitted hexagon refined as free rotating group:
 C88A(C93A,C92A,C91A,C90A,C89A), C88(C93,C92,C91,C90,C89), C52A(C53A,C54A,C55A,
 C56A,C57A)
6.e Idealised Me refined as rotating group:
 C302(H30A,H30B,H30C), C402(H40A,H40B,H40C)
;
_shelx_res_checksum              96402
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
'Empirical correction (ABSPACK) includes: - Absorption correction using spherical harmonics - Frame scaling'
_oxdiff_exptl_absorpt_empirical_full_max 6.739
_oxdiff_exptl_absorpt_empirical_full_min 0.604