#------------------------------------------------------------------------------ #$Date: 2023-09-18 14:42:39 +0300 (Mon, 18 Sep 2023) $ #$Revision: 286386 $ #$URL: file:///home/coder/svn-repositories/cod/cif/2/31/22/2312293.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_2312293 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 0.1511 _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 0.29 _refine_diff_density_min -0.17 _refine_ls_extinction_coef 51(9) _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 2.2725 _refine_ls_goodness_of_fit_ref 2.0282 _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 0.1531 _refine_ls_R_factor_gt 0.1395 _refine_ls_shift/su_max 0.0285 _refine_ls_shift/su_mean 0.0060 _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 0.3365 _refine_ls_wR_factor_ref 0.3447 _reflns_number_gt 845 _reflns_number_total 1127 _reflns_threshold_expression I>3\s(I) _cod_data_source_file pl5027.cif _cod_data_source_block L-alanine_model2 _cod_original_cell_volume 420.85(14) _cod_original_sg_symbol_Hall 'P 2xab;2ybc;2zac' _cod_database_code 2312293 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 -0.1250(5) 0.7273(10) 0.4159(3) Uani 0.0189(12) 4 1 d . . . O2 O -0.2612(5) 0.4452(8) 0.3155(3) Uani 0.0149(10) 4 1 d . . . C1 C -0.1014(6) 0.5553(10) 0.3595(3) Uani 0.0115(11) 4 1 d . . . C2 C 0.1928(7) 0.2661(12) 0.4095(4) Uani 0.0202(14) 4 1 d . . . N1 N 0.3142(5) 0.6531(8) 0.3624(3) Uani 0.0143(10) 4 1 d . . . C3 C 0.1454(5) 0.4701(10) 0.3391(3) Uani 0.0132(12) 4 1 d . . . H1c3 H 0.163455 0.422061 0.25614 Uani 0.0158 4 1 d . . . H1c2 H 0.365811 0.212 0.39729 Uani 0.0242 4 1 d . . . H2c2 H 0.077385 0.135045 0.387752 Uani 0.0242 4 1 d . . . H3c2 H 0.168404 0.308475 0.492782 Uani 0.0242 4 1 d . . . H1n1 H 0.287995 0.781509 0.309918 Uani 0.0172 4 1 d . . . H2n1 H 0.291942 0.707962 0.43975 Uani 0.0172 4 1 d . . . H3n1 H 0.477069 0.594049 0.353404 Uani 0.0172 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 0.0126(10) 0.024(3) 0.0203(15) 0.0004(14) 0.0005(11) -0.0059(14) O2 O 0.0062(8) 0.016(2) 0.0228(15) -0.0003(12) 0.0001(10) -0.0058(12) C1 C 0.0075(11) 0.012(3) 0.0150(16) -0.0012(15) -0.0023(12) -0.0003(14) C2 C 0.0159(14) 0.022(4) 0.0223(18) -0.0003(20) -0.0030(14) -0.0054(17) N1 N 0.0085(10) 0.015(3) 0.0197(15) -0.0017(13) 0.0011(12) 0.0040(12) C3 C 0.0075(11) 0.018(3) 0.0138(15) 0.0025(15) -0.0011(12) -0.0020(14) H1c3 H 0.009026 0.021987 0.016535 0.003056 -0.001353 -0.002415 H1c2 H 0.019108 0.026869 0.026742 -0.000334 -0.003591 -0.006475 H2c2 H 0.019108 0.026869 0.026742 -0.000334 -0.003591 -0.006475 H3c2 H 0.019108 0.026869 0.026742 -0.000334 -0.003591 -0.006475 H1n1 H 0.010244 0.017696 0.023592 -0.002059 0.001328 0.004762 H2n1 H 0.010244 0.017696 0.023592 -0.002059 0.001328 0.004762 H3n1 H 0.010244 0.017696 0.023592 -0.002059 0.001328 0.004762 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 . . . 126.1(4) O1 C1 C3 . . . 117.7(4) O2 C1 C3 . . . 116.2(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 . . . 109.9(3) C1 C3 N1 . . . 109.6(4) C1 C3 H1c3 . . . 109.69 C2 C3 N1 . . . 111.0(3) C2 C3 H1c3 . . . 108.17 N1 C3 H1c3 . . . 108.49 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 . . 1.243(8) O2 C1 . . 1.254(6) C1 C3 . . 1.533(5) C2 C3 . . 1.514(8) C2 H1c2 . . 1.06 C2 H2c2 . . 1.06 C2 H3c2 . . 1.06 N1 C3 . . 1.489(6) 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 2.42 3.443(6) 162.97 N1 H1n1 O2 . . 3_555 1.01 1.83 2.804(6) 162.19 N1 H2n1 O1 . . 4_566 1.01 1.87 2.828(5) 156.87 N1 H3n1 O2 . . 1_655 1.01 1.81 2.805(5) 167.05 N1 H3n1 C1 . . 1_655 1.01 2.45 3.424(4) 162.94