#------------------------------------------------------------------------------ #$Date: 2023-09-18 14:42:39 +0300 (Mon, 18 Sep 2023) $ #$Revision: 286386 $ #$URL: file:///home/coder/svn-repositories/cod/cif/2/31/22/2312292.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/. The original data for this entry # were provided by IUCr Journals, http://journals.iucr.org/. # # The file may be used within the scientific community so long as # proper attribution is given to the journal article from which the # data were obtained. # data_2312292 loop_ _publ_author_name 'Khouchen, Malak' 'Klar, Paul Benjamin' 'Chintakindi, Hrushikesh' 'Suresh, Ashwin' 'Palatinus, Lukas' _publ_section_title ; Optimal estimated standard uncertainties of reflection intensities for kinematical refinement from 3D electron diffraction data ; _journal_coeditor_code PL5027 _journal_issue 5 _journal_name_full 'Acta Crystallographica Section A Foundations and Advances' _journal_page_first 427 _journal_page_last 439 _journal_paper_doi 10.1107/S2053273323005053 _journal_volume 79 _journal_year 2023 _chemical_absolute_configuration rm _chemical_formula_sum 'C3 H7 N O2' _chemical_formula_weight 89.1 _chemical_name_common DL-alanine _chemical_name_systematic DL-alanine _space_group_IT_number 19 _space_group_name_Hall 'P 2ac 2ab' _space_group_name_H-M_alt 'P 21 21 21' _symmetry_cell_setting orthorhombic _symmetry_Int_Tables_number 19 _symmetry_space_group_name_Hall 'P 2ac 2ab' _symmetry_space_group_name_H-M 'P 21 21 21' _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 5.7733(11) _cell_length_b 5.9524(12) _cell_length_c 12.2465(2) _cell_measurement_reflns_used 3422 _cell_measurement_temperature 100 _cell_measurement_theta_max 1.44 _cell_measurement_theta_min 0.12 _cell_volume 420.85(12) _computing_cell_refinement PETS2 _computing_data_collection 'self-written scripts, OLYMPUS iTEM' _computing_data_reduction PETS2 _computing_molecular_graphics 'VESTA 3' _computing_structure_refinement Jana2020 _computing_structure_solution superflip _diffrn_ambient_temperature 100 _diffrn_detector ASI _diffrn_measured_fraction_theta_full 0.84 _diffrn_measured_fraction_theta_max 0.55 _diffrn_measurement_device 'TEM FEI Tecnai G2 20' _diffrn_measurement_method 'continuous-rotation 3D ED' _diffrn_measurement_specimen_support 'holey carbon grid' _diffrn_radiation_probe electron _diffrn_radiation_source 'Lab6 cathode' _diffrn_radiation_type 'electrons 200 keV' _diffrn_radiation_wavelength 0.0251 _diffrn_reflns_av_R_equivalents 0.111 _diffrn_reflns_av_unetI/netI 0.0779 _diffrn_reflns_limit_h_max 11 _diffrn_reflns_limit_h_min -11 _diffrn_reflns_limit_k_max 9 _diffrn_reflns_limit_k_min -9 _diffrn_reflns_limit_l_max 22 _diffrn_reflns_limit_l_min -24 _diffrn_reflns_number 3422 _diffrn_reflns_theta_full 1.09 _diffrn_reflns_theta_max 1.44 _diffrn_reflns_theta_min 0.12 _exptl_crystal_density_diffrn 1.4061 _exptl_crystal_description 'irregular shape' _exptl_crystal_F_000 69.628 _refine_diff_density_max 0.17 _refine_diff_density_min -0.21 _refine_ls_extinction_coef 15(2) _refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^ _refine_ls_extinction_method 'SHELXL-2017/1 (Sheldrick, 2015)' _refine_ls_goodness_of_fit_gt 5.9096 _refine_ls_goodness_of_fit_ref 5.3504 _refine_ls_hydrogen_treatment constr _refine_ls_number_constraints 63 _refine_ls_number_parameters 56 _refine_ls_number_reflns 1127 _refine_ls_number_restraints 0 _refine_ls_R_factor_all 0.1571 _refine_ls_R_factor_gt 0.1392 _refine_ls_shift/su_max 0.0313 _refine_ls_shift/su_mean 0.0062 _refine_ls_structure_factor_coef Fsqd _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.02P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme sigma _refine_ls_wR_factor_gt 0.3359 _refine_ls_wR_factor_ref 0.3376 _reflns_number_gt 922 _reflns_number_total 1127 _reflns_threshold_expression I>3\s(I) _cod_data_source_file pl5027.cif _cod_data_source_block L-alanine_model1 _cod_original_cell_volume 420.85(14) _cod_original_sg_symbol_Hall 'P 2xab;2ybc;2zac' _cod_database_code 2312292 loop_ _space_group_symop_id _space_group_symop_operation_xyz 1 x,y,z 2 -x+1/2,-y,z+1/2 3 -x,y+1/2,-z+1/2 4 x+1/2,-y+1/2,-z loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_adp_type _atom_site_U_iso_or_equiv _atom_site_site_symmetry_multiplicity _atom_site_occupancy _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group O1 O -0.1255(7) 0.7261(9) 0.4150(3) Uani 0.0162(10) 4 1 d . . . O2 O -0.2631(6) 0.4407(9) 0.3153(3) Uani 0.0157(9) 4 1 d . . . C1 C -0.1014(8) 0.5568(10) 0.3600(3) Uani 0.0108(10) 4 1 d . . . C2 C 0.1960(9) 0.2671(12) 0.4091(4) Uani 0.0186(15) 4 1 d . . . N1 N 0.3148(7) 0.6573(8) 0.3611(3) Uani 0.0136(12) 4 1 d . . . C3 C 0.1445(8) 0.4699(11) 0.3390(3) Uani 0.0156(13) 4 1 d . . . H1c3 H 0.159651 0.418564 0.256373 Uani 0.0187 4 1 d . . . H1c2 H 0.366103 0.209284 0.39265 Uani 0.0223 4 1 d . . . H2c2 H 0.075479 0.137857 0.391252 Uani 0.0223 4 1 d . . . H3c2 H 0.182477 0.311882 0.492639 Uani 0.0223 4 1 d . . . H1n1 H 0.299026 0.708295 0.439396 Uani 0.0163 4 1 d . . . H2n1 H 0.28167 0.78754 0.310604 Uani 0.0163 4 1 d . . . H3n1 H 0.477652 0.601256 0.348072 Uani 0.0163 4 1 d . . . loop_ _atom_site_aniso_label _atom_site_aniso_type_symbol _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 O1 O 0.0103(13) 0.022(2) 0.0167(11) -0.0059(16) 0.0005(14) -0.0059(12) O2 O 0.0047(11) 0.025(2) 0.0170(11) 0.0024(15) 0.0027(10) -0.0097(11) C1 C 0.0067(15) 0.015(2) 0.0104(11) 0.006(2) 0.0009(14) -0.0019(13) C2 C 0.016(2) 0.017(3) 0.0227(18) 0.003(2) -0.0078(19) -0.0084(15) N1 N 0.0105(15) 0.013(3) 0.0177(13) 0.0074(17) -0.0001(13) -0.0055(11) C3 C 0.0069(15) 0.027(3) 0.0124(12) 0.0013(18) -0.0017(14) -0.0013(15) H1c3 H 0.008277 0.032903 0.01487 0.001522 -0.00202 -0.001569 H1c2 H 0.019111 0.020468 0.027206 0.004181 -0.009388 -0.010068 H2c2 H 0.019111 0.020468 0.027206 0.004181 -0.009388 -0.010068 H3c2 H 0.019111 0.020468 0.027206 0.004181 -0.009388 -0.010068 H1n1 H 0.012596 0.015156 0.021192 0.008933 -0.00006 -0.006614 H2n1 H 0.012596 0.015156 0.021192 0.008933 -0.00006 -0.006614 H3n1 H 0.012596 0.015156 0.021192 0.008933 -0.00006 -0.006614 loop_ _atom_type_symbol _atom_type_scat_source C International_Tables_Vol_C H International_Tables_Vol_C N International_Tables_Vol_C O International_Tables_Vol_C loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_2 _geom_angle_site_symmetry_3 _geom_angle O1 C1 O2 . . . 126.6(5) O1 C1 C3 . . . 118.5(4) O2 C1 C3 . . . 114.9(5) C3 C2 H1c2 . . . 109.47 C3 C2 H2c2 . . . 109.47 C3 C2 H3c2 . . . 109.47 H1c2 C2 H2c2 . . . 109.47 H1c2 C2 H3c2 . . . 109.47 H2c2 C2 H3c2 . . . 109.47 C3 N1 H1n1 . . . 109.47 C3 N1 H2n1 . . . 109.47 C3 N1 H3n1 . . . 109.47 H1n1 N1 H2n1 . . . 109.47 H1n1 N1 H3n1 . . . 109.47 H2n1 N1 H3n1 . . . 109.47 C1 C3 C2 . . . 110.9(4) C1 C3 N1 . . . 108.9(5) C1 C3 H1c3 . . . 109.51 C2 C3 N1 . . . 111.1(4) C2 C3 H1c3 . . . 107.23 N1 C3 H1c3 . . . 109.28 loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_site_symmetry_1 _geom_bond_site_symmetry_2 _geom_bond_distance O1 C1 . . 1.221(7) O2 C1 . . 1.284(6) C1 C3 . . 1.533(7) C2 C3 . . 1.511(9) C2 H1c2 . . 1.06 C2 H2c2 . . 1.06 C2 H3c2 . . 1.06 N1 C3 . . 1.512(7) N1 H1n1 . . 1.01 N1 H2n1 . . 1.01 N1 H3n1 . . 1.01 C3 H1c3 . . 1.06 loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_site_symmetry_D _geom_hbond_site_symmetry_H _geom_hbond_site_symmetry_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA C3 H1c3 O1 . . 3_545 1.06 2.40 3.434(6) 164.89 N1 H1n1 O1 . . 4_566 1.01 1.88 2.849(5) 160.68 N1 H2n1 O2 . . 3_555 1.01 1.79 2.757(6) 158.01 N1 H3n1 O2 . . 1_655 1.01 1.82 2.813(6) 166.71 N1 H3n1 C1 . . 1_655 1.01 2.45 3.423(6) 161.77