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_1552286
_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_formula_moiety
'C126 H112 N12 O6 S3 Zn2, 4(Cl O4), 5.75(C2 H3 N), O'
_chemical_formula_sum            'C137.5 H129.25 Cl4 N17.75 O23 S3 Zn2'
_chemical_formula_weight         2767.05
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_symmetry_space_group_name_Hall  '-C 2yc'
_symmetry_space_group_name_H-M   'C 1 2/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2018-12-28
_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                 104.4640(10)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   38.9929(5)
_cell_length_b                   22.5983(2)
_cell_length_c                   36.9118(6)
_cell_measurement_reflns_used    61039
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      67.2280
_cell_measurement_theta_min      2.2700
_cell_volume                     31494.8(7)
_computing_cell_refinement
'CrysAlisPro, Agilent Technologies, Version 1.171.37.35 (release 13-08-2014 CrysAlis171 .NET) (compiled Aug 13 2014,18:06:01)'
_computing_data_collection
'CrysAlisPro, Agilent Technologies, Version 1.171.37.35 (release 13-08-2014 CrysAlis171 .NET) (compiled Aug 13 2014,18:06:01)'
_computing_data_reduction
'CrysAlisPro, Agilent Technologies, Version 1.171.37.35 (release 13-08-2014 CrysAlis171 .NET) (compiled Aug 13 2014,18:06:01)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_details
;
  #__ type_ start__ end____ width___ exp.time_ 1 omega -107.00 73.00 1.0000 5.0000 omega____ theta____ kappa____ phi______ frames - -17.0000 50.0000 60.0000 180 
  #__ type_ start__ end____ width___ exp.time_ 2 omega -88.00 -32.00 1.0000 5.0000 omega____ theta____ kappa____ phi______ frames - -17.0000 20.0000 -180.0000 56 
  #__ type_ start__ end____ width___ exp.time_ 3 omega -179.00 0.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 -180.0000 179 
  #__ type_ start__ end____ width___ exp.time_ 4 omega -164.00 -17.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 -90.0000 147 
  #__ type_ start__ end____ width___ exp.time_ 5 omega -179.00 0.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 90.0000 179 
  #__ type_ start__ end____ width___ exp.time_ 6 omega -179.00 -19.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 40.0000 -120.0000 160 
  #__ type_ start__ end____ width___ exp.time_ 7 omega -137.00 -47.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 -30.0000 90 
  #__ type_ start__ end____ width___ exp.time_ 8 omega -179.00 0.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 -150.0000 179 
  #__ type_ start__ end____ width___ exp.time_ 9 omega -128.00 -47.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 50.0000 -60.0000 81 
  #__ type_ start__ end____ width___ exp.time_ 10 omega -162.00 -132.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 30.0000 60.0000 30 
  #__ type_ start__ end____ width___ exp.time_ 11 omega -168.00 -46.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 150.0000 122 
  #__ type_ start__ end____ width___ exp.time_ 12 omega -165.00 -107.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 30.0000 58 
  #__ type_ start__ end____ width___ exp.time_ 13 omega -165.00 -19.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 -120.0000 146 
  #__ type_ start__ end____ width___ exp.time_ 14 omega -164.00 -139.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 0.0000 25 
  #__ type_ start__ end____ width___ exp.time_ 15 omega -166.00 -141.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 -60.0000 25 
  #__ type_ start__ end____ width___ exp.time_ 16 omega -162.00 -136.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 60.0000 60.0000 26 
  #__ type_ start__ end____ width___ exp.time_ 17 omega -128.00 -103.00 1.0000 30.0000 omega____ theta____ kappa____ phi______ frames - -90.0000 0.0000 -180.0000 25 
;
_diffrn_measurement_device       'abstract diffractometer'
_diffrn_measurement_device_type
'dtrek-CrysAlisPro-abstract goniometer imported rigaku-d*trek images'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_UB_11      0.0365083000
_diffrn_orient_matrix_UB_12      -0.0151754000
_diffrn_orient_matrix_UB_13      -0.0064947000
_diffrn_orient_matrix_UB_21      -0.0041436000
_diffrn_orient_matrix_UB_22      -0.0644303000
_diffrn_orient_matrix_UB_23      0.0118689000
_diffrn_orient_matrix_UB_31      -0.0177343000
_diffrn_orient_matrix_UB_32      -0.0163229000
_diffrn_orient_matrix_UB_33      -0.0409330000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0614
_diffrn_reflns_av_unetI/netI     0.0286
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       46
_diffrn_reflns_limit_h_min       -46
_diffrn_reflns_limit_k_max       27
_diffrn_reflns_limit_k_min       -27
_diffrn_reflns_limit_l_max       43
_diffrn_reflns_limit_l_min       -44
_diffrn_reflns_number            210313
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.399
_diffrn_reflns_theta_max         67.399
_diffrn_reflns_theta_min         2.278
_diffrn_source                   'Enhance (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.904
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.68487
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'CrysAlisPro, Agilent Technologies, Version 1.171.37.35 (release 13-08-2014 CrysAlis171 .NET) (compiled Aug 13 2014,18:06:01) 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    1.167
_exptl_crystal_F_000             11508
_exptl_crystal_size_max          0.29
_exptl_crystal_size_mid          0.11
_exptl_crystal_size_min          0.1
_refine_diff_density_max         1.130
_refine_diff_density_min         -0.828
_refine_diff_density_rms         0.096
_refine_ls_extinction_coef       0.000039(8)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2016/6 (Sheldrick 2016)'
_refine_ls_goodness_of_fit_ref   1.013
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1776
_refine_ls_number_reflns         28259
_refine_ls_number_restraints     327
_refine_ls_restrained_S_all      1.058
_refine_ls_R_factor_all          0.1052
_refine_ls_R_factor_gt           0.0892
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1835P)^2^+56.2583P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2612
_refine_ls_wR_factor_ref         0.2800
_reflns_Friedel_coverage         0.000
_reflns_number_gt                21550
_reflns_number_total             28259
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c9sc03532j3.cif
_cod_data_source_block           ds6
_cod_original_formula_sum        'C137.50 H129.25 Cl4 N17.75 O23 S3 Zn2'
_cod_database_code               1552286
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         'C63 H120 N12 O22 Cl4 Zn2'
_reflns_odcompleteness_completeness 99.81
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     67.29
_olex2_refinement_description
;
The asymmetric unit contains the metallohelice, four perchlorates and seven molecules of acetonitrile.
Acetonitriles N1A-C2A, N1B-C2B andN1C-C2C were modelled at full occupancy.
Acetonitrile N1D-C2D was modeled at 75% occupancy.
Acetonitrile N1F-C2F and N1G-C2G were modelled at a half occupancy and refined iostropically.
Another acetonitrile was modelled over two closely related positions (N1E-C2E and N1H-C2H) at 
50% occupancy and refined isotropically.
Perchlorate Cl20 was modelled as disordered over two positions about Cl20. The occupancies were linked 
to a free variable which refined to a ratio of 82:18. The minor component oxygens were refined isotropically.
Perchlorate Cl30 was modelled as disordered over two positions about Cl30. The occupancies were originally 
linked to a free variable but once this had settled were fixed at a ratio of 75:25 for the final stages of 
the refinement. The minor component oxygens were refined isotropically.
Perchorate Cl40 was modelled over two positions. The occupancy of these two perchlorate positions 
(Cl40 and l4A) was fixed at 50%. This disordered model was also composed of water molecules that shared that 
space when a perchlorate was not present. One perchlorate component Cl40 occupied the same location as 
water O1C (50% occupancy).
The other perchlorate Cl4A occupied the same location as two closely related waters O1A (25% occupancy) and 
O1B (50%) occupancy.  
To clarify, one part of the disordered model has perchlorate Cl40 and waters O1A and O1B and the other part 
has perchlorate Cl4A and water O1B. No hydrogens were located on these waters and the oxygens were 
refined isotropically.
Several DFIX, DANG and SIMU restraints were used to give the disordered components reasonably 
bond lengths, angles and thermal parameters

The structure contained large solvent accessible voids.
The solvent masking algorithm in Olex2 was used to treat the electron density from solvent molecules that were 
not located as a diffuse contribution to the overall scattering without specific atom positions. 

The total solvent accessible volume was 4248 Angstroms cubed (13.5% of cell volume). The analysis identifies 
four voids and below is their postulated contents that could fill the volume and account for the electron 
density contribution.

The voids are tabulated below with the following volumes and electron counts and coordinates

Void   #Grid points  Vol/A^3    Vol/% of cell     electron count        Centre of mass (frac)   
   1       139838    1062.0      3.4              258.7                 (-0.000,-0.353, 0.250)              
   2       139838    1062.0      3.4              258.3                 ( 0.000, 0.353, 0.750)                                                   
   3       139838    1062.0      3.4              258.7                 ( 0.500, 0.147, 0.250)  
   4       139838    1062.0      3.4              258.3                 ( 0.500, 0.853, 0.750)

Volumes of acetonitrile calculated simply using the vdw radius of each atom type 

Approximate volume of acetonitrile 80 Angstroms cubed
Electron count for acetonitrile is 22. 

An approximate value for the contents of the void based on these values is given below.
As the voids are nearly identical, the calculation shown below was used for the four voids

Void 1
Void volume and electron count from Olex2
Volume 1062   electron count 259

Possible Void 1 contents
11 x acetonitrile
Calculated volume 880 and electron count 242

That is a total of 44 molecules of acetonitrile filling the voids that would account for the calculated 
electron density using the solvent masking algorithm in Olex2.

1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 N1F-C2F
 1.2 with sigma of 0.02
 Cl4A-O41A = Cl4A-O42A = Cl4A-O43A
 1.414 with sigma of 0.02
 Cl4A-O44A
 1.414 with sigma of 0.004
 Cl20-O21 = Cl20-O22 = Cl20-O23 = Cl20-O24
 1.414 with sigma of 0.02
 Cl20-O21A = Cl20-O22A = Cl20-O23A = Cl20-O24A
 1.414 with sigma of 0.02
 Cl30-O31 = Cl30-O32 = Cl30-O33 = Cl30-O34
 1.414 with sigma of 0.02
 Cl30-O31A = Cl30-O32A = Cl30-O33A = Cl30-O34A
 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
 O21-O22 = O21-O23 = O21-O24 = O22-O23 = O22-O24 = O23-O24
 2.309 with sigma of 0.04
 O21A-O22A = O21A-O23A = O21A-O24A = O22A-O23A = O22A-O24A = O23A-O24A
 2.309 with sigma of 0.04
 O31-O32 = O31-O33 = O31-O34 = O32-O33 = O32-O34 = O33-O34
 2.309 with sigma of 0.04
 O31A-O32A = O31A-O33A = O31A-O34A = O32A-O33A = O32A-O34A = O33A-O34A
 2.309 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
N8 \\sim C80 \\sim C81 \\sim C82 \\sim C83 \\sim C84: within 1.7A with sigma of
0.004 and sigma for terminal atoms of 0.008
N1A \\sim C2A \\sim C3A: within 1.7A with sigma of 0.002 and sigma for terminal
atoms of 0.004
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
Cl20 \\sim O21 \\sim O22 \\sim O23 \\sim O24 \\sim O21A \\sim O22A \\sim O23A
\\sim O24A: within 1.7A with sigma of 0.004 and sigma for terminal atoms of
0.008
Cl30 \\sim O31 \\sim O32 \\sim O33 \\sim O34 \\sim O31A \\sim O32A \\sim O33A
\\sim O34A: within 1.7A with sigma of 0.002 and sigma for terminal atoms of
0.004
Cl40 \\sim O41 \\sim O42 \\sim O44 \\sim O43: within 1.7A with sigma of 0.01
and sigma for terminal atoms of 0.02
C2D \\sim C3D \\sim N1D: within 1.7A with sigma of 0.002 and sigma for terminal
atoms of 0.004
4. Others
 Sof(O21A)=Sof(O22A)=Sof(O23A)=Sof(O24A)=1-FVAR(1)
 Sof(O21)=Sof(O22)=Sof(O23)=Sof(O24)=FVAR(1)
 Fixed Sof: O31(0.75) O32(0.75) O33(0.75) O34(0.75) Cl40(0.5) O41(0.5)
 O42(0.5) O44(0.5) O43(0.5) Cl4A(0.5) O41A(0.5) O42A(0.5) O43A(0.5) O44A(0.5)
 O31A(0.25) O32A(0.25) O33A(0.25) O34A(0.25) C2D(0.75) C3D(0.75) H3DA(0.75)
 H3DB(0.75) H3DC(0.75) N1D(0.75) N1E(0.5) C2E(0.5) C3E(0.5) H3EA(0.5) H3EB(0.5)
 H3EC(0.5) N1F(0.5) C2F(0.5) C3F(0.5) H3FA(0.5) H3FB(0.5) H3FC(0.5) C3G(0.5)
 H3GA(0.5) H3GB(0.5) H3GC(0.5) C2G(0.5) N1G(0.5) N1H(0.5) C2H(0.5) C3H(0.5)
 H3HA(0.5) H3HB(0.5) H3HC(0.5) O1A(0.25) O1B(0.5) O1C(0.25)
5.a Ternary CH refined with riding coordinates:
 C7(H7), C30(H30), C49(H49), C72(H72), C91(H91), C114(H114)
5.b Secondary CH2 refined with riding coordinates:
 C14(H14A,H14B), C15(H15A,H15B), C28(H28A,H28B), C29(H29A,H29B), C56(H56A,
 H56B), C57(H57A,H57B), C70(H70A,H70B), C71(H71A,H71B), C98(H98A,H98B),
 C99(H99A,H99B), C112(H11A,H11B), C113(H11C,H11D)
5.c Me refined with riding coordinates:
 C3F(H3FA,H3FB,H3FC)
5.d Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C4(H4), C6(H6), C9(H9), C10(H10), C0AA(H0AA),
 C12(H12), C13(H13), C17(H17), C1AA(H1AA), C20(H20), C21(H21), C23(H23),
 C24(H24), C26(H26), C27(H27), C32(H32), C33(H33), C34(H34), C35(H35), C36(H36),
  C37(H37), C39(H39), C40(H40), C41(H41), C42(H42), C43(H43), C44(H44),
 C45(H45), C46(H46), C48(H48), C51(H51), C52(H52), C53(H53), C54(H54), C55(H55),
  C59(H59), C60(H60), C62(H62), C63(H63), C65(H65), C66(H66), C68(H68),
 C69(H69), C76(H76), C77(H77), C78(H78), C79(H79), C81(H81), C82(H82), C83(H83),
  C84(H84), C85(H85), C86(H86), C87(H87), C88(H88), C90(H90), C93(H93),
 C94(H94), C95(H95), C96(H96), C97(H97), C101(H101), C102(H102), C104(H104),
 C105(H105), C107(H107), C108(H108), C110(H110), C111(H111), C116(H116),
 C117(H117), C118(H118), C119(H119), C120(H120), C121(H121), C123(H123),
 C124(H124), C125(H125), C126(H126)
5.e Idealised Me refined as rotating group:
 C3D(H3DA,H3DB,H3DC), C3C(H3CA,H3CB,H3CC), C3B(H3BA,H3BB,H3BC), C3A(H3AA,H3AB,
 H3AC), C3E(H3EA,H3EB,H3EC), C3G(H3GA,H3GB,H3GC), C3H(H3HA,H3HB,H3HC)
;
_shelx_res_checksum              84412
_shelx_fab_checksum              85769
_olex2_submission_special_instructions 'No special instructions were received'