Bottom-up design of peptide shapes in water using oligomers of N-methyl-l/d-alanine
Morimoto, Jumpei; Yokomine, Marin; Shiratori, Yota; Ueda, Takumi; Nakamuro, Takayuki; Takaba, Kiyofumi; Maki-Yonekura, Saori; Umezawa, Koji; Miyanishi, Koichiro; Fukuda, Yasuhiro; Watanabe, Takumu; Suga, Mayuko; Inayoshi, Ayumi; Yoshida, Takuya; Mizukami, Wataru; Takeuchi, Koh; Yonekura, Koji; Nakamura, Eiichi; Sando, Shinsuke; Chemical Science 16 (2025) 10512–10522; doi:10.1039/D5SC01483B

data_1574569
_publ_section_title
;
 Bottom-up design of peptide shapes in water using oligomers of
 N-methyl-l/d-alanine
;
_journal_issue                   23
_journal_name_full               'Chemical Science'
_journal_page_first              10512
_journal_page_last               10522
_journal_paper_doi               10.1039/D5SC01483B
_journal_volume                  16
_journal_year                    2025
_chemical_absolute_configuration unk
_chemical_formula_moiety         '2(C19 H34 N4 O5), 0.25(H2 O)'
_chemical_formula_sum            'C38 H68 N8 O10'
_chemical_formula_weight         797.00
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   mixed
_audit_creation_date             2023-01-17
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6408)
;
_audit_update_record
;
2023-04-25 deposited with the CCDC.	2025-04-24 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   5.98460(10)
_cell_length_b                   22.8259(3)
_cell_length_c                   31.5688(4)
_cell_measurement_reflns_used    10254
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      71.7200
_cell_measurement_theta_min      3.4010
_cell_volume                     4312.42(11)
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_diffrn_ambient_temperature      293(2)
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.986
_diffrn_measurement_device_type  'XtaLAB AFC10 (RCD3): quarter-chi single'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0427
_diffrn_reflns_av_unetI/netI     0.0458
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.986
_diffrn_reflns_limit_h_max       7
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       25
_diffrn_reflns_limit_k_min       -27
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -37
_diffrn_reflns_number            18304
_diffrn_reflns_point_group_measured_fraction_full 0.971
_diffrn_reflns_point_group_measured_fraction_max 0.945
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         72.254
_diffrn_reflns_theta_min         2.389
_exptl_absorpt_coefficient_mu    0.731
_exptl_crystal_density_diffrn    1.228
_exptl_crystal_description       plate
_exptl_crystal_F_000             1728
_refine_diff_density_max         0.224
_refine_diff_density_min         -0.205
_refine_diff_density_rms         0.053
_refine_ls_abs_structure_details
;
 Flack x determined using 2874 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.06(9)
_refine_ls_extinction_coef       0.00076(16)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.045
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     534
_refine_ls_number_reflns         8052
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.045
_refine_ls_R_factor_all          0.0422
_refine_ls_R_factor_gt           0.0390
_refine_ls_shift/su_max          0.066
_refine_ls_shift/su_mean         0.001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0720P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1021
_refine_ls_wR_factor_ref         0.1040
_reflns_Friedel_coverage         0.677
_reflns_Friedel_fraction_full    0.932
_reflns_Friedel_fraction_max     0.890
_reflns_number_gt                7476
_reflns_number_total             8052
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc01483b3.cif
_cod_data_source_block           nma-dimer-ll
_cod_depositor_comments
'Adding full bibliography for 1574566--1574569.cif.'
_cod_database_code               1574569
_shelx_shelxl_version_number     2018/3
_olex2_refinement_description
;
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, All O(H,H) groups
2. Others
 Fixed Sof: O11(0.25) H11C(0.25) H11D(0.25)
3.a Free rotating group:
 O11(H11C,H11D)
3.b Ternary CH refined with riding coordinates:
 C23(H23), C8(H8), C27(H27), C4(H4)
3.c Secondary CH2 refined with riding coordinates:
 C30(H30A,H30B), C11(H11A,H11B), C12(H12A,H12B), C14(H14A,H14B), C13(H13A,
 H13B), C31(H31A,H31B), C33(H33A,H33B), C32(H32A,H32B)
3.d Idealised Me refined as rotating group:
 C24(H24A,H24B,H24C), C22(H22A,H22B,H22C), C7(H7A,H7B,H7C), C17(H17A,H17B,
 H17C), C20(H20A,H20B,H20C), C26(H26A,H26B,H26C), C9(H9A,H9B,H9C), C19(H19A,
 H19B,H19C), C5(H5A,H5B,H5C), C18(H18A,H18B,H18C), C28(H28A,H28B,H28C),
 C38(H38A,H38B,H38C), C36(H36A,H36B,H36C), C37(H37A,H37B,H37C), C3(H3A,H3B,H3C),
  C1(H1A,H1B,H1C)
;
_shelx_res_checksum              85360
_olex2_submission_special_instructions 'No special instructions were received'