Dear All, Thank you all for your help. I’ve tried several approaches to input this file, including changing the format to mmCIF, importing it as coordinates, and checking the restraints in the file. However, I am still unable to install the experimental ligand structure into the protein. It seems that COOT or JLigand cannot read the restraints from the CIF file.
I’m wondering if anyone has faced a similar problem before, and if there is a way to input the experimental structure and save its restraints so that it can be refined with the overall protein structure in Refmac? I’ve attached the original CIF file here for your reference (in .txt format). Sincerely, Martin ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
####################################################################### # # This file contains crystal structure data downloaded from the # Cambridge Structural Database (CSD) hosted by the Cambridge # Crystallographic Data Centre (CCDC). # # Full information about CCDC data access policies and citation # guidelines are available at http://www.ccdc.cam.ac.uk/access/V1 # # Audit and citation data items may have been added by the CCDC. # Please retain this information to preserve the provenance of # this file and to allow appropriate attribution of the data. # ####################################################################### data_twin5 _audit_block_doi 10.5517/ccryflp _database_code_depnum_ccdc_archive 'CCDC 713483' loop_ _citation_id _citation_doi _citation_year 1 10.1016/j.dyepig.2009.03.001 2009 _audit_update_record ; 2008-12-13 deposited with the CCDC. 2024-08-19 downloaded from the CCDC. ; _audit_creation_method SHELXL-97 _chemical_name_systematic ; ? ; _chemical_name_common ? _chemical_melting_point ? _chemical_formula_moiety 'C9 H7 B F2 N2' _chemical_formula_sum 'C9 H7 B F2 N2' _chemical_formula_weight 191.98 loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' B B 0.0013 0.0007 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' F F 0.0171 0.0103 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting Monoclinic _symmetry_space_group_name_H-M C2/c _symmetry_space_group_name_Hall '-C 2yc' loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, y, -z+1/2' 'x+1/2, y+1/2, z' '-x+1/2, y+1/2, -z+1/2' '-x, -y, -z' 'x, -y, z-1/2' '-x+1/2, -y+1/2, -z' 'x+1/2, -y+1/2, z-1/2' _cell_length_a 10.126(4) _cell_length_b 10.196(4) _cell_length_c 17.143(6) _cell_angle_alpha 90.00 _cell_angle_beta 102.285(6) _cell_angle_gamma 90.00 _cell_volume 1729.5(11) _cell_formula_units_Z 8 _cell_measurement_temperature 296(2) _cell_measurement_reflns_used 32 _cell_measurement_theta_min 2.45 _cell_measurement_theta_max 12.33 _exptl_crystal_description plate _exptl_crystal_colour orange _exptl_crystal_size_max 0.20 _exptl_crystal_size_mid 0.20 _exptl_crystal_size_min 0.04 _exptl_crystal_density_meas 'not measured' _exptl_crystal_density_diffrn 1.475 _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 784 _exptl_absorpt_coefficient_mu 0.119 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_correction_T_min 0.9766 _exptl_absorpt_correction_T_max 0.9953 _exptl_absorpt_process_details twinabs _exptl_special_details ; ? ; _diffrn_ambient_temperature 296(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'fine-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'CCD area detector' _diffrn_measurement_method 'phi and omega scans' _diffrn_detector_area_resol_mean ? _diffrn_standards_number ? _diffrn_standards_interval_count ? _diffrn_standards_interval_time ? _diffrn_standards_decay_% ? _diffrn_reflns_number 3845 _diffrn_reflns_av_R_equivalents 0.0000 _diffrn_reflns_av_sigmaI/netI 0.2541 _diffrn_reflns_limit_h_min -11 _diffrn_reflns_limit_h_max 11 _diffrn_reflns_limit_k_min -11 _diffrn_reflns_limit_k_max 11 _diffrn_reflns_limit_l_min -19 _diffrn_reflns_limit_l_max 20 _diffrn_reflns_theta_min 2.43 _diffrn_reflns_theta_max 24.77 _reflns_number_total 3845 _reflns_number_gt 1360 _reflns_threshold_expression >2sigma(I) _computing_data_collection 'Bruker APEX II' _computing_cell_refinement 'Bruker APEX II' _computing_data_reduction 'Bruker APEX II' _computing_structure_solution 'SHELXS-97 (Sheldrick, 1990)' _computing_structure_refinement 'SHELXL-97 (Sheldrick, 1997)' _computing_molecular_graphics 'Bruker SHELXTL' _computing_publication_material 'Bruker SHELXTL' _refine_special_details ; Refinement of F^2^ against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The threshold expression of F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.1025P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_ls_hydrogen_treatment refall _refine_ls_extinction_method SHELXL _refine_ls_extinction_coef 0.0053(16) _refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^ _refine_ls_number_reflns 3845 _refine_ls_number_parameters 129 _refine_ls_number_restraints 0 _refine_ls_R_factor_all 0.2818 _refine_ls_R_factor_gt 0.1029 _refine_ls_wR_factor_ref 0.2803 _refine_ls_wR_factor_gt 0.1990 _refine_ls_goodness_of_fit_ref 1.004 _refine_ls_restrained_S_all 1.004 _refine_ls_shift/su_max 0.000 _refine_ls_shift/su_mean 0.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_occupancy _atom_site_symmetry_multiplicity _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group F1 F 0.0587(3) 0.1257(4) 0.09256(19) 0.0773(12) Uani 1 1 d . . . F2 F -0.0926(3) 0.2839(3) 0.10355(19) 0.0796(13) Uani 1 1 d . . . N1 N 0.0270(6) 0.3022(5) -0.0036(3) 0.0592(14) Uani 1 1 d . . . N2 N 0.1431(5) 0.3421(4) 0.1373(3) 0.0582(15) Uani 1 1 d . . . B1 B 0.0302(8) 0.2605(8) 0.0838(5) 0.062(2) Uani 1 1 d . . . C1 C -0.0617(7) 0.2670(7) -0.0700(5) 0.076(2) Uani 1 1 d . . . H1A H -0.1374 0.2152 -0.0703 0.092 Uiso 1 1 calc R . . C2 C -0.0270(8) 0.3169(7) -0.1378(4) 0.076(2) Uani 1 1 d . . . H2A H -0.0726 0.3045 -0.1904 0.092 Uiso 1 1 calc R . . C3 C 0.0882(8) 0.3883(6) -0.1116(4) 0.0696(19) Uani 1 1 d . . . H3A H 0.1350 0.4356 -0.1434 0.084 Uiso 1 1 calc R . . C4 C 0.1228(7) 0.3776(6) -0.0288(4) 0.0583(17) Uani 1 1 d . . . C5 C 0.2233(6) 0.4346(6) 0.0274(4) 0.0634(18) Uani 1 1 d . . . H5A H 0.2867 0.4867 0.0099 0.076 Uiso 1 1 calc R . . C6 C 0.2352(6) 0.4185(6) 0.1085(4) 0.0562(17) Uani 1 1 d . . . C7 C 0.3230(7) 0.4738(6) 0.1728(5) 0.068(2) Uani 1 1 d . . . H7A H 0.3941 0.5301 0.1700 0.082 Uiso 1 1 calc R . . C8 C 0.2876(7) 0.4315(7) 0.2418(4) 0.075(2) Uani 1 1 d . . . H8A H 0.3286 0.4536 0.2939 0.090 Uiso 1 1 calc R . . C9 C 0.1766(7) 0.3482(6) 0.2168(4) 0.071(2) Uani 1 1 d . . . H9A H 0.1324 0.3033 0.2510 0.085 Uiso 1 1 calc R . . loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 F1 0.086(3) 0.061(3) 0.086(3) 0.008(2) 0.023(2) -0.007(2) F2 0.055(2) 0.103(3) 0.089(3) -0.004(2) 0.0317(19) -0.010(2) N1 0.057(4) 0.057(4) 0.065(4) 0.006(3) 0.017(3) 0.000(3) N2 0.053(4) 0.058(4) 0.067(4) 0.008(3) 0.024(3) -0.007(3) B1 0.053(6) 0.058(6) 0.080(6) 0.011(5) 0.026(5) 0.002(5) C1 0.064(5) 0.088(6) 0.077(5) -0.003(4) 0.015(4) -0.014(4) C2 0.083(6) 0.090(6) 0.059(5) 0.000(4) 0.023(4) 0.003(5) C3 0.077(6) 0.066(5) 0.070(5) 0.012(4) 0.026(4) -0.002(4) C4 0.049(5) 0.059(5) 0.068(5) 0.008(4) 0.015(4) 0.002(4) C5 0.053(5) 0.062(5) 0.079(5) 0.018(4) 0.023(4) -0.003(4) C6 0.059(5) 0.052(4) 0.058(5) 0.002(4) 0.013(4) -0.006(4) C7 0.063(5) 0.066(5) 0.082(5) -0.004(4) 0.031(4) -0.007(4) C8 0.055(5) 0.088(6) 0.076(5) -0.016(4) 0.000(4) 0.004(4) C9 0.069(5) 0.100(6) 0.047(5) 0.019(4) 0.018(4) 0.003(4) _geom_special_details ; All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag F1 B1 1.405(8) . ? F2 B1 1.378(7) . ? N1 C1 1.340(7) . ? N1 C4 1.377(7) . ? N1 B1 1.551(8) . ? N2 C9 1.335(6) . ? N2 C6 1.384(6) . ? N2 B1 1.547(8) . ? C1 C2 1.382(7) . ? C1 H1A 0.9300 . ? C2 C3 1.367(7) . ? C2 H2A 0.9300 . ? C3 C4 1.393(7) . ? C3 H3A 0.9300 . ? C4 C5 1.373(7) . ? C5 C6 1.380(7) . ? C5 H5A 0.9300 . ? C6 C7 1.381(7) . ? C7 C8 1.375(7) . ? C7 H7A 0.9300 . ? C8 C9 1.401(7) . ? C8 H8A 0.9300 . ? C9 H9A 0.9300 . ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag C1 N1 C4 105.8(5) . . ? C1 N1 B1 128.2(6) . . ? C4 N1 B1 125.8(6) . . ? C9 N2 C6 107.1(5) . . ? C9 N2 B1 128.7(6) . . ? C6 N2 B1 124.1(5) . . ? F2 B1 F1 108.6(6) . . ? F2 B1 N2 110.7(6) . . ? F1 B1 N2 110.7(6) . . ? F2 B1 N1 110.8(6) . . ? F1 B1 N1 109.5(6) . . ? N2 B1 N1 106.6(6) . . ? N1 C1 C2 111.8(6) . . ? N1 C1 H1A 124.1 . . ? C2 C1 H1A 124.1 . . ? C3 C2 C1 105.7(6) . . ? C3 C2 H2A 127.1 . . ? C1 C2 H2A 127.1 . . ? C2 C3 C4 107.8(6) . . ? C2 C3 H3A 126.1 . . ? C4 C3 H3A 126.1 . . ? C5 C4 N1 118.9(6) . . ? C5 C4 C3 132.1(7) . . ? N1 C4 C3 108.8(6) . . ? C4 C5 C6 123.3(6) . . ? C4 C5 H5A 118.3 . . ? C6 C5 H5A 118.3 . . ? C5 C6 N2 120.3(6) . . ? C5 C6 C7 131.3(7) . . ? N2 C6 C7 108.3(6) . . ? C8 C7 C6 108.5(6) . . ? C8 C7 H7A 125.8 . . ? C6 C7 H7A 125.8 . . ? C7 C8 C9 105.5(6) . . ? C7 C8 H8A 127.3 . . ? C9 C8 H8A 127.3 . . ? N2 C9 C8 110.7(6) . . ? N2 C9 H9A 124.7 . . ? C8 C9 H9A 124.7 . . ? loop_ _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4 _geom_torsion _geom_torsion_site_symmetry_1 _geom_torsion_site_symmetry_2 _geom_torsion_site_symmetry_3 _geom_torsion_site_symmetry_4 _geom_torsion_publ_flag C9 N2 B1 F2 53.6(9) . . . . ? C6 N2 B1 F2 -130.6(6) . . . . ? C9 N2 B1 F1 -66.9(8) . . . . ? C6 N2 B1 F1 108.9(6) . . . . ? C9 N2 B1 N1 174.2(5) . . . . ? C6 N2 B1 N1 -10.0(8) . . . . ? C1 N1 B1 F2 -53.0(9) . . . . ? C4 N1 B1 F2 131.8(6) . . . . ? C1 N1 B1 F1 66.8(8) . . . . ? C4 N1 B1 F1 -108.4(6) . . . . ? C1 N1 B1 N2 -173.5(6) . . . . ? C4 N1 B1 N2 11.3(8) . . . . ? C4 N1 C1 C2 0.0(7) . . . . ? B1 N1 C1 C2 -175.9(6) . . . . ? N1 C1 C2 C3 -0.9(8) . . . . ? C1 C2 C3 C4 1.4(7) . . . . ? C1 N1 C4 C5 176.1(5) . . . . ? B1 N1 C4 C5 -7.8(9) . . . . ? C1 N1 C4 C3 0.9(7) . . . . ? B1 N1 C4 C3 177.0(5) . . . . ? C2 C3 C4 C5 -175.9(7) . . . . ? C2 C3 C4 N1 -1.5(7) . . . . ? N1 C4 C5 C6 1.1(9) . . . . ? C3 C4 C5 C6 175.1(6) . . . . ? C4 C5 C6 N2 -0.1(9) . . . . ? C4 C5 C6 C7 -175.4(6) . . . . ? C9 N2 C6 C5 -177.9(5) . . . . ? B1 N2 C6 C5 5.6(9) . . . . ? C9 N2 C6 C7 -1.6(6) . . . . ? B1 N2 C6 C7 -178.2(6) . . . . ? C5 C6 C7 C8 176.3(6) . . . . ? N2 C6 C7 C8 0.6(7) . . . . ? C6 C7 C8 C9 0.6(7) . . . . ? C6 N2 C9 C8 2.0(7) . . . . ? B1 N2 C9 C8 178.4(6) . . . . ? C7 C8 C9 N2 -1.6(7) . . . . ? _diffrn_measured_fraction_theta_max 0.987 _diffrn_reflns_theta_full 24.77 _diffrn_measured_fraction_theta_full 0.987 _refine_diff_density_max 0.181 _refine_diff_density_min -0.178 _refine_diff_density_rms 0.049 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
