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#\#CIF_1.0 ################################################################################ # # # This CIF is a part of the B-IncStrDB # # (Bilbao Incommensurate Structures Database) # # http://www.cryst.ehu.eus/bincstrdb/ # # # # Please note that the structure of the CIF file may differ from the one # # deposited, as it may have been modified to comply with the standard. The # # file has been validated against official dictionaries as well as local # # dictionaries including non-standard data names used by SHELXL (Sheldrick, # # G. M. (2008). Acta Cryst. A 64, 112-122) and JANA (Petricek, V., Dusek, M. # # and Palatinus, L. (2014), Z. Kristallogr. 229, 345-352). # # # # For comments and/or criticisms, please e-mail to administrador-bcs@ehu.es # # # ################################################################################ data_global _publ_contact_author_name 'Gemmi, Mauro' _publ_contact_author_address ;Center for Nanotechnology Innovation @NEST Istituto Italiano di Tecnologia Piazza S. Silvestro, 12 Pisa 56127 Italy ; _publ_contact_author_email mauro.gemmi@iit.it loop_ _publ_author_name _publ_author_address 'Lanza, Arianna E.' ;Center for Nanotechnology Innovation @NEST Istituto Italiano di Tecnologia Piazza S. Silvestro, 12 Pisa 56127 Italy ; 'Gemmi, Mauro' ;Center for Nanotechnology Innovation @NEST Istituto Italiano di Tecnologia Piazza S. Silvestro, 12 Pisa 56127 Italy ; 'Bindi, Luca' ;Dipartimento di Scienze della Terra University of Florence Via La Pira Firenze I-50121 Italy ; 'Mugnaioli, Enrico' ;Center for Nanotechnology Innovation @NEST Istituto Italiano di Tecnologia Piazza S. Silvestro, 12 Pisa 56127 Italy ; 'Paar, Werner H.' ;Department of Chemistry and Physics of Materials University of Salzburg Salzburg Austria ; _publ_section_title ;Daliranite, PbHgAs~2~S~5~: determination of the incommensurately modulated structure and revision of the chemical formula ; _journal_date_recd_electronic 2019-03-19 _journal_date_accepted 2019-05-20 _journal_coeditor_code DK5082SUP1 _journal_paper_category FA _journal_techeditor_code B190734 _iucr_compatibility_tag ACTA95 _journal_name_full 'Acta Crystallographica, Section B' _journal_volume 75 _journal_year 2019 _journal_page_first 711 _journal_page_last 716 _journal_paper_doi https://doi.org/10.1107/S2052520619007340 data_average _database_code_depnum_ccdc_archive 'CCDC 1917352' _chemical_name_common daliranite _chemical_formula_moiety 'As2 Hg Pb S5' _chemical_formula_sum 'As2 Hg Pb S5' _chemical_formula_weight 717.9 _chemical_absolute_configuration ? _space_group_crystal_system orthorhombic _space_group_name_H-M_alt Pnma _space_group_IT_number 62 loop_ _space_group_symop_id _space_group_symop_operation_xyz 1 'x, y, z' 2 '-x, -y, -z' 3 '-x+1/2, -y, z+1/2' 4 'x+1/2, y, -z+1/2' 5 'x+1/2, -y+1/2, -z+1/2' 6 '-x+1/2, y+1/2, z+1/2' 7 '-x, y+1/2, -z' 8 'x, -y+1/2, z' _cell_length_a 21.246(5) _cell_length_b 4.2897(9) _cell_length_c 9.5257(12) _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_volume 868.2(3) _cell_formula_units_Z 4 _cell_measurement_reflns_used 2033 _cell_measurement_theta_min 0.05 _cell_measurement_theta_max 1.2 _cell_measurement_temperature 298 _exptl_crystal_type_of_structure cryst _exptl_crystal_density_diffrn 5.4927 _exptl_crystal_F_000 1232 _exptl_crystal_description needle _exptl_crystal_size_max 0.0002 _exptl_crystal_size_mid 0.0001 _exptl_crystal_size_min 0.0001 _exptl_crystal_colour orange _exptl_absorpt_correction_type none loop_ _exptl_crystal_face_index_h _exptl_crystal_face_index_k _exptl_crystal_face_index_l _exptl_crystal_face_perp_dist ? ? ? ? _diffrn_ambient_temperature 298 _diffrn_source_voltage 120 _diffrn_radiation_type electron _diffrn_source LaB6 _diffrn_radiation_wavelength 0.0335 _diffrn_measurement_device 'ZEISS Libra 120' _diffrn_measurement_device_type TEM _diffrn_detector Timepix2 _exptl_special_details 'data have been collected by precession assisted 3D electron diffraction' _diffrn_reflns_number 10451 _diffrn_reflns_theta_min 0.05 _diffrn_reflns_theta_max 1.2 _diffrn_reflns_theta_full 0.95 _diffrn_measured_fraction_theta_max 0.57 _diffrn_measured_fraction_theta_full 0.79 _diffrn_reflns_av_R_equivalents 0.3349 _diffrn_reflns_av_unetI/netI 0.0384 _diffrn_reflns_limit_h_min -20 _diffrn_reflns_limit_h_max 20 _diffrn_reflns_limit_k_min -4 _diffrn_reflns_limit_k_max 3 _diffrn_reflns_limit_l_min -8 _diffrn_reflns_limit_l_max 10 _diffrn_radiation_probe electron _reflns_number_total 562 _reflns_number_gt 401 _reflns_threshold_expression I>3\s(I) _refine_ls_structure_factor_coef F _refine_ls_R_factor_gt 0.2435 _refine_ls_wR_factor_gt 0.2946 _refine_ls_R_factor_all 0.3222 _refine_ls_wR_factor_ref 0.3025 _refine_ls_goodness_of_fit_ref 13.93 _refine_ls_goodness_of_fit_gt 16.27 _refine_ls_number_reflns 562 _refine_ls_number_parameters 34 _refine_ls_weighting_scheme sigma _refine_ls_weighting_details w=1/(\s^2^(F)+0.0001F^2^) _refine_ls_shift/su_max 0.0002 _refine_ls_shift/su_mean 0.0001 _refine_diff_density_max 0.45 _refine_diff_density_min -0.40 loop_ _atom_type_symbol _atom_type_scat_source As International_Tables_Vol_C Hg International_Tables_Vol_C Pb International_Tables_Vol_C S International_Tables_Vol_C _computing_data_reduction 'PETS 2.0 (Palatinus et al., 2011)' _computing_structure_solution 'SIR2014 (Burla et al., 2015)' _computing_structure_refinement 'Jana2006 (Petricek et al., 2014)' _computing_molecular_graphics 'Vesta (Momma & Izumi, 2011)' 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_posn _atom_site_disorder_assembly _atom_site_disorder_group Pb1 Pb 0.2886(7) 0.25 1.3368(8) Uani 0.083(6) 4 1 d ? ? ? Hg1 Hg 0.4150(6) 0.25 0.9831(7) Uani 0.065(5) 4 1 d ? ? ? As1 As 0.1286(13) 0.356(3) 1.1428(18) Uiso 0.030(6) 8 0.5 d ? ? ? As2 As 0.0526(12) 0.356(3) 0.8089(16) Uiso 0.019(6) 8 0.5 d ? ? ? S1 S 0.2233(15) 0.25 1.060(2) Uiso 0.034(7) 4 1 d ? ? ? S2 S 0.1437(15) 0.25 0.690(2) Uiso 0.036(7) 4 1 d ? ? ? S3 S 0.3337(16) 0.25 0.805(2) Uiso 0.042(7) 4 1 d ? ? ? S4 S 0.4132(13) 0.25 1.4762(19) Uiso 0.019(6) 4 1 d ? ? ? S5 S 0.4954(15) 0.25 1.160(2) Uiso 0.040(7) 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 Pb1 Pb 0.137(16) 0.101(8) 0.011(5) 0 -0.002332 0 Hg1 Hg 0.118(14) 0.069(6) 0.009(5) 0 0.001652 0 loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_site_ssg_symmetry_1 _geom_bond_site_ssg_symmetry_2 _geom_bond_distance _geom_bond_publ_flag Pb1 S1 ? ? 2.982(17) ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle_site_ssg_symmetry_1 _geom_angle_site_ssg_symmetry_2 _geom_angle_site_ssg_symmetry_3 _geom_angle _geom_angle_publ_flag Pb1 S1 S2 ? ? ? 177.9 ? _vrf_PLAT213_I ; PROBLEM: High R1 Value .................................. 0.24 Report RESPONSE: High R1 values are expected in electron diffraction data. ; data_modulated _database_code_depnum_ccdc_archive 'CCDC 1917353' _chemical_formula_moiety 'As2 Hg Pb S5' _chemical_formula_sum 'As2 Hg Pb S5' _chemical_formula_weight 717.9 _chemical_absolute_configuration ? _space_group_crystal_system orthorhombic _space_group_name_H-M_alt Pnma _space_group_ssg_name Pnma(00\g)0s0 loop_ _space_group_symop_ssg_id _space_group_symop_ssg_operation_algebraic 1 x1,x2,x3,x4 2 -x1+1/2,-x2,x3+1/2,x4+1/2 3 -x1,x2+1/2,-x3,-x4+1/2 4 x1+1/2,-x2+1/2,-x3+1/2,-x4 5 -x1,-x2,-x3,-x4 6 x1+1/2,x2,-x3+1/2,-x4+1/2 7 x1,-x2+1/2,x3,x4+1/2 8 -x1+1/2,x2+1/2,x3+1/2,x4 _cell_length_a 21.246(5) _cell_length_b 4.2897(9) _cell_length_c 9.5257(12) _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_volume 868.2(3) _cell_modulation_dimension 1 loop_ _cell_wave_vector_seq_id _cell_wave_vector_x _cell_wave_vector_y _cell_wave_vector_z 1 0.000000 0.000000 0.262(2) _cell_formula_units_Z 4 _cell_measurement_reflns_used 10451 _cell_measurement_theta_min 0.05 _cell_measurement_theta_max 1.2 _cell_measurement_temperature 298 _exptl_crystal_type_of_structure mod _exptl_crystal_density_diffrn 5.4927 _exptl_crystal_F_000 1232 _exptl_crystal_description needle _exptl_crystal_size_max 0.0002 _exptl_crystal_size_mid 0.0001 _exptl_crystal_size_min 0.0001 _exptl_crystal_colour orange _exptl_absorpt_correction_type none loop_ _exptl_crystal_face_index_h _exptl_crystal_face_index_k _exptl_crystal_face_index_l _exptl_crystal_face_perp_dist ? ? ? ? _diffrn_ambient_temperature 298 _diffrn_source_voltage 120 _diffrn_radiation_type electron _diffrn_source LaB6 _diffrn_radiation_wavelength 0.0335 _diffrn_measurement_device 'ZEISS Libra 120' _diffrn_measurement_device_type TEM _diffrn_detector Timepix2 _exptl_special_details 'data have been collected by precession assisted 3D electron diffraction' _diffrn_reflns_number 10451 _diffrn_reflns_theta_min 0.05 _diffrn_reflns_theta_max 1.2 _diffrn_reflns_theta_full 0.95 _diffrn_measured_fraction_theta_max 0.57 _diffrn_measured_fraction_theta_full 0.79 _diffrn_reflns_av_R_equivalents 0.3349 _diffrn_reflns_av_unetI/netI 0.0384 _diffrn_reflns_limit_h_min -20 _diffrn_reflns_limit_h_max 20 _diffrn_reflns_limit_k_min -4 _diffrn_reflns_limit_k_max 3 _diffrn_reflns_limit_l_min -8 _diffrn_reflns_limit_l_max 10 _diffrn_reflns_limit_index_m_1_min -1 _diffrn_reflns_limit_index_m_1_max 1 _diffrn_radiation_probe electron _reflns_number_total 1503 _reflns_number_gt 981 _reflns_threshold_expression I>3\s(I) _refine_ls_structure_factor_coef F _refine_ls_R_factor_gt 0.2715 _refine_ls_wR_factor_gt 0.2989 _refine_ls_R_factor_all 0.3818 _refine_ls_wR_factor_ref 0.3097 _refine_ls_goodness_of_fit_ref 10.70 _refine_ls_goodness_of_fit_gt 12.87 _refine_ls_number_reflns 1503 _refine_ls_number_parameters 38 _refine_ls_weighting_scheme sigma _refine_ls_weighting_details w=1/(\s^2^(F)+0.0001F^2^) _refine_ls_shift/su_max 0.0009 _refine_ls_shift/su_mean 0.0003 _refine_diff_density_max 0.45 _refine_diff_density_min -0.40 _refine_ls_extinction_method none loop_ _atom_type_symbol _atom_type_scat_source As International_Tables_Vol_C Hg International_Tables_Vol_C Pb International_Tables_Vol_C S International_Tables_Vol_C _computing_data_reduction 'PETS 2.0 (Palatinus et al., 2011)' _computing_structure_solution 'SIR2014 (Burla et al., 2015)' _computing_structure_refinement 'Jana2006 (Petricek et al., 2014)' _computing_molecular_graphics 'Vesta (Momma & Izumi, 2011)' 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_posn _atom_site_disorder_assembly _atom_site_disorder_group Pb1 Pb 0.2885(5) 0.25 1.3367(5) Uani 0.061(4) 4 1 d ? ? ? Hg1 Hg 0.4149(5) 0.25 0.9835(5) Uani 0.063(4) 4 1 d ? ? ? As1 As 0.1285(8) 0.371(2) 1.1430(11) Uiso 0.031(3) 8 0.5 d ? ? ? As2 As 0.0517(7) 0.365(2) 0.8082(10) Uiso 0.027(3) 8 0.5 d ? ? ? S1 S 0.2236(10) 0.25 1.0596(15) Uiso 0.027(4) 4 1 d ? ? ? S2 S 0.1430(9) 0.25 0.6898(14) Uiso 0.019(4) 4 1 d ? ? ? S3 S 0.3344(11) 0.25 0.8066(15) Uiso 0.026(4) 4 1 d ? ? ? S4 S 0.4134(8) 0.25 1.4756(12) Uiso 0.007(4) 4 1 d ? ? ? S5 S 0.4962(10) 0.25 1.1610(15) Uiso 0.030(5) 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 Pb1 Pb 0.132(11) 0.033(4) 0.018(3) 0 -0.003(4) 0 Hg1 Hg 0.122(10) 0.060(4) 0.006(3) 0 0.002(3) 0 loop_ _atom_site_Fourier_wave_vector_seq_id _jana_atom_site_Fourier_wave_vector_q1_coeff 1 1 loop_ _atom_site_occ_special_func_atom_site_label _atom_site_occ_special_func_crenel_c _atom_site_occ_special_func_crenel_w As1 0.390(5) 0.5 As2 0.314(5) 0.5 loop_ _atom_site_displace_Fourier_id _atom_site_displace_Fourier_atom_site_label _atom_site_displace_Fourier_axis _atom_site_displace_Fourier_wave_vector_seq_id Pb1x1 Pb1 x 1 Pb1y1 Pb1 y 1 Pb1z1 Pb1 z 1 Hg1x1 Hg1 x 1 Hg1y1 Hg1 y 1 Hg1z1 Hg1 z 1 S1x1 S1 x 1 S1y1 S1 y 1 S1z1 S1 z 1 S2x1 S2 x 1 S2y1 S2 y 1 S2z1 S2 z 1 S3x1 S3 x 1 S3y1 S3 y 1 S3z1 S3 z 1 S4x1 S4 x 1 S4y1 S4 y 1 S4z1 S4 z 1 S5x1 S5 x 1 S5y1 S5 y 1 S5z1 S5 z 1 loop_ _atom_site_displace_Fourier_param_id _atom_site_displace_Fourier_param_cos _atom_site_displace_Fourier_param_sin Pb1x1 0 0 Pb1y1 -0.0284 0.0865 Pb1z1 0 0 Hg1x1 0 0 Hg1y1 0.0393 0.0529 Hg1z1 0 0 S1x1 0 0 S1y1 -0.0211 0.0555 S1z1 0 0 S2x1 0 0 S2y1 0.0111 0.0498 S2z1 0 0 S3x1 0 0 S3y1 0.0547 0.0185 S3z1 0 0 S4x1 0 0 S4y1 0.0147 0.0209 S4z1 0 0 S5x1 0 0 S5y1 0.0279 -0.0315 S5z1 0 0 loop_ _atom_site_U_Fourier_id _atom_site_U_Fourier_atom_site_label _atom_site_U_Fourier_tens_elem _atom_site_U_Fourier_wave_vector_seq_id Pb1U111 Pb1 U11 1 Pb1U221 Pb1 U22 1 Pb1U331 Pb1 U33 1 Pb1U121 Pb1 U12 1 Pb1U131 Pb1 U13 1 Pb1U231 Pb1 U23 1 Hg1U111 Hg1 U11 1 Hg1U221 Hg1 U22 1 Hg1U331 Hg1 U33 1 Hg1U121 Hg1 U12 1 Hg1U131 Hg1 U13 1 Hg1U231 Hg1 U23 1 loop_ _atom_site_U_Fourier_param_id _atom_site_U_Fourier_param_cos _atom_site_U_Fourier_param_sin Pb1U111 0 0 Pb1U221 0 0 Pb1U331 0 0 Pb1U121 0.015246 0.011714 Pb1U131 0 0 Pb1U231 0 0 Hg1U111 0 0 Hg1U221 0 0 Hg1U331 0 0 Hg1U121 0 -0.008135 Hg1U131 0 0 Hg1U231 0 0 loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_site_ssg_symmetry_1 _geom_bond_site_ssg_symmetry_2 _geom_bond_distance_av _geom_bond_distance_min _geom_bond_distance_max _geom_bond_publ_flag Pb1 S1 ? ? 2.982(17) 2.979(17) 2.986(17) ? Pb1 S1 ? 2_5555 3.031(11) 2.912(11) 3.151(11) ? Pb1 S1 ? 2_5655 3.029(11) 2.912(11) 3.151(11) ? Pb1 S2 ? 2_5555 2.948(13) 2.808(13) 3.087(13) ? Pb1 S2 ? 2_5655 2.945(13) 2.808(13) 3.087(13) ? Pb1 S3 ? 2_5555 3.403(19) 3.13(2) 3.69(2) ? Pb1 S3 ? 2_5655 3.398(19) 3.13(2) 3.69(2) ? Pb1 S4 ? ? 2.975(19) 2.963(19) 2.985(19) ? Hg1 S2 ? 2_5555 3.159(12) 3.114(12) 3.205(12) ? Hg1 S2 ? 2_5655 3.159(12) 3.114(12) 3.205(12) ? Hg1 S3 ? ? 2.40(2) 2.40(2) 2.40(2) ? Hg1 S5 ? ? 2.43(2) 2.42(2) 2.45(2) ? Hg1 S5 ? 3_6475 3.184(16) 2.880(17) 3.501(17) ? Hg1 S5 ? 3_6575 3.179(16) 2.880(17) 3.501(17) ? As1 S1 ? ? 2.20(3) 2.19(3) 2.26(3) ? As1 S3 ? 2_5555 3.287(13) 3.056(14) 3.397(14) ? As1 S3 ? 2_5655 2.308(16) 2.224(17) 2.495(17) ? As1 S4 ? 2_5545 3.212(13) 3.141(13) 3.316(13) ? As1 S4 ? 2_5645 2.460(15) 2.377(15) 2.518(15) ? As1 S5 ? 4_4575 3.41(2) 3.39(2) 3.44(2) ? As2 S2 ? ? 2.28(2) 2.26(2) 2.32(2) ? As2 S4 ? 2_5545 3.155(12) 3.080(12) 3.259(12) ? As2 S4 ? 2_5645 2.426(14) 2.342(14) 2.489(14) ? As2 S5 ? 2_5545 3.239(14) 3.083(14) 3.309(14) ? As2 S5 ? 2_5645 2.328(17) 2.272(17) 2.455(17) ? S1 S3 ? ? 3.37(3) 3.37(3) 3.38(3) ? S1 S3 ? 2_5555 3.423(18) 3.164(19) 3.695(19) ? S1 S3 ? 2_5655 3.419(18) 3.164(19) 3.695(19) ? S2 S5 ? 2_5545 3.67(2) 3.47(3) 3.88(3) ? S2 S5 ? 2_5645 3.67(2) 3.47(3) 3.88(3) ? S4 S5 ? ? 3.48(2) 3.48(2) 3.48(2) ? _vrf_PLAT213_I ; PROBLEM: _symmetry_equiv_pos_as_xyz not in the CIF RESPONSE: This entry is replaced by _space_group_symop_ssg_operation_algebraic ;