0.039526 0.000000 0.000000 0.000000 0.024832 0.000000 0.000000 0.000000 0.015413 0.00000 0.00000 0.00000 McDonough, M. El-Sagheer, A.H. Brown, T. Schofield, C.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.300 40.270 64.880 C10 H16 N3 O8 P 337.223 n 2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) DNA linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer N 1 N P N 2 N O N 3 N O N 4 N O N 5 N C N 6 R C N 7 N O N 8 S C N 9 N O N 10 N C N 11 R C N 12 N N N 13 N C N 14 N O N 15 N N N 16 N C N 17 N N N 18 N C N 19 N C N 20 N O N 21 N C N 22 N O N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N O N 40 N P N 41 N O N 42 N O N 43 N O N 44 N C N 45 R C N 46 N O N 47 S C N 48 N O N 49 N C N 50 R C Y 51 N N Y 52 N C Y 53 N N Y 54 N C Y 55 N C N 56 N N Y 57 N N Y 58 N C Y 59 N N Y 60 N C N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N O N 76 N P N 77 N O N 78 N O N 79 N O N 80 N C N 81 R C N 82 N O N 83 S C N 84 N O N 85 N C N 86 R C N 87 N N N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N C N 94 N C N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 N C N 120 R C Y 121 N N Y 122 N C Y 123 N N Y 124 N C N 125 N C N 126 N O N 127 N N N 128 N C N 129 N N N 130 N N Y 131 N C N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N O N 147 N P N 148 N O N 149 N O N 150 N O N 151 N C N 152 R C N 153 N O N 154 S C N 155 N O N 156 N C N 157 R C N 158 N N N 159 N C N 160 N O N 161 N N N 162 N C N 163 N O N 164 N C N 165 N C N 166 N C N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N O N 183 N H N 184 N H N 185 N MG N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N doub N 13 N sing N 14 N sing N 15 N doub N 16 N sing N 17 N doub N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing Y 63 N sing Y 64 N sing Y 65 N doub N 66 N sing Y 67 N sing Y 68 N sing Y 69 N doub N 70 N sing Y 71 N doub N 72 N sing N 73 N sing Y 74 N sing Y 75 N doub N 76 N sing Y 77 N sing N 78 N sing N 79 N sing N 80 N doub N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing Y 136 N sing Y 137 N sing Y 138 N doub N 139 N sing Y 140 N sing N 141 N sing Y 142 N doub N 143 N doub N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N doub N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing N 180 N sing N 181 N doub N 182 N sing N 183 N sing N 184 N doub N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing UK Chem. Commun. (Camb.) 1364-548X 50 1794 1796 10.1039/c3cc48151d 24287551 Structural insights into how 5-hydroxymethylation influences transcription factor binding. 2014 10.2210/pdb4c5x/pdb pdb_00004c5x 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 MIRRORS PIXEL 2011-07-24 DECTRIS PILATUS 2M SI (111) DOUBLE CRYSTAL SINGLE WAVELENGTH M x-ray 1 0.917300 1.0 I04-1 Diamond 0.917300 SYNCHROTRON DIAMOND BEAMLINE I04-1 3693.418 5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3' DICKERSON-DREW SEQUENCE DODECAMER 2 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 136 nat water no yes (DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(5HC)(DG)(DC)(DG) CGCGAATTXGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 1 2.02 39 NONE 7.5 40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5 3.091 1 19 A 1 B 24 0.439 A_DC1:DG24_B 1 -15.782 0.225 0.128 -0.120 4.303 1 19 A 2 B 23 -2.879 A_DG2:DC23_B 2 -15.308 -0.185 0.461 -0.170 -2.183 1 19 A 3 B 22 -0.668 A_DC3:DG22_B 3 -1.685 0.170 0.009 -0.168 13.886 1 19 A 4 B 21 -0.372 A_DG4:5HC21_B 4 -9.088 -0.286 0.053 -0.150 7.473 1 20 A 5 B 20 1.748 A_DA5:DT20_B 5 -16.447 0.021 0.005 -0.109 1.935 1 20 A 6 B 19 4.163 A_DA6:DT19_B 6 -15.937 0.041 0.076 -0.068 -0.190 1 20 A 7 B 18 4.282 A_DT7:DA18_B 7 -17.927 -0.010 0.103 -0.103 -2.709 1 20 A 8 B 17 3.434 A_DT8:DA17_B 8 -13.438 -0.079 0.012 -0.175 -9.340 1 19 A 9 B 16 -1.119 A_5HC9:DG16_B 9 -11.130 0.213 -0.108 -0.138 5.365 1 19 A 10 B 15 3.096 A_DG10:DC15_B 10 -9.142 -0.142 0.203 -0.098 4.090 1 19 A 11 B 14 -2.345 A_DC11:DG14_B 11 -17.682 0.148 0.102 -0.181 5.075 1 19 A 12 B 13 -0.238 A_DG12:DC13_B 12 -7.070 -0.130 0.389 -0.053 3.213 35.573 A A 1 2 10.557 B B 24 23 3.236 6.411 -0.139 0.151 AA_DC1DG2:DC23DG24_BB 1 -2.788 4.591 34.901 -0.682 -0.177 3.443 42.167 A A 2 3 -10.962 B B 23 22 3.537 -7.835 0.745 0.502 AA_DG2DC3:DG22DC23_BB 2 3.848 -5.385 41.294 1.568 -0.608 2.971 25.003 A A 3 4 18.045 B B 22 21 3.027 7.689 0.086 0.285 AA_DC3DG4:5HC21DG22_BB 3 -0.213 0.501 23.808 -1.491 -0.259 3.438 38.531 A A 4 5 0.500 B B 21 20 3.424 0.330 -0.506 -0.018 AA_DG4DA5:DT205HC21_BB 4 -1.267 1.920 38.510 -0.070 0.603 3.294 39.452 A A 5 6 1.601 B B 20 19 3.303 1.081 -0.005 -0.212 AA_DA5DA6:DT19DT20_BB 5 -1.434 2.124 39.413 -0.443 -0.164 3.280 31.977 A A 6 7 -4.527 B B 19 18 3.246 -2.492 -0.023 -0.577 AA_DA6DT7:DA18DT19_BB 6 -0.045 0.082 31.882 -0.598 0.034 3.248 34.973 A A 7 8 -1.135 B B 18 17 3.244 -0.682 -0.006 -0.388 AA_DT7DT8:DA17DA18_BB 7 1.404 -2.336 34.940 -0.544 0.220 3.390 42.181 A A 8 9 -2.818 B B 17 16 3.396 -2.026 -0.128 -0.240 AA_DT85HC9:DG16DA17_BB 8 2.693 -3.746 42.052 -0.117 0.466 3.029 26.168 A A 9 10 13.357 B B 16 15 3.051 5.972 0.629 0.838 AA_5HC9DG10:DC15DG16_BB 9 -4.044 9.045 25.172 0.314 -2.429 3.190 44.853 A A 10 11 -13.160 B B 15 14 3.348 -9.962 -1.259 0.631 AA_DG10DC11:DG14DC15_BB 10 -2.022 2.671 43.744 1.742 1.465 3.217 32.889 A A 11 12 11.071 B B 14 13 3.214 6.230 -0.036 0.327 AA_DC11DG12:DC13DG14_BB 11 -1.700 3.022 32.266 -0.479 -0.225 citation citation_author chem_comp_atom chem_comp_bond database_2 pdbx_database_status pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Database references Database references Database references Data collection Database references Derived calculations Other Refinement description 1 0 2013-10-02 1 1 2013-12-11 1 2 2014-02-12 1 3 2018-02-21 1 4 2023-12-20 _citation.journal_abbrev _citation.journal_id_ISSN _citation.page_last _citation.pdbx_database_id_DOI _citation.title _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_sf _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5-METHYLCYSTOSINE MODIFICATION ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA PDBE Y PDBE 2013-09-16 REL REL MG MAGNESIUM ION HOH water 32630 SYNTHETIC CONSTRUCT sample 1BNA PDB ENRTY 1BNA PDB experimental model MG 101 2 MG MG 101 A HOH 2001 3 HOH HOH 2001 A HOH 2002 3 HOH HOH 2002 A HOH 2003 3 HOH HOH 2003 A HOH 2004 3 HOH HOH 2004 A HOH 2005 3 HOH HOH 2005 A HOH 2006 3 HOH HOH 2006 A HOH 2007 3 HOH HOH 2007 A HOH 2008 3 HOH HOH 2008 A HOH 2009 3 HOH HOH 2009 A HOH 2010 3 HOH HOH 2010 A HOH 2011 3 HOH HOH 2011 A HOH 2012 3 HOH HOH 2012 A HOH 2013 3 HOH HOH 2013 A HOH 2014 3 HOH HOH 2014 A HOH 2015 3 HOH HOH 2015 A HOH 2016 3 HOH HOH 2016 A HOH 2017 3 HOH HOH 2017 A HOH 2018 3 HOH HOH 2018 A HOH 2019 3 HOH HOH 2019 A HOH 2020 3 HOH HOH 2020 A HOH 2021 3 HOH HOH 2021 A HOH 2022 3 HOH HOH 2022 A HOH 2023 3 HOH HOH 2023 A HOH 2024 3 HOH HOH 2024 A HOH 2025 3 HOH HOH 2025 A HOH 2026 3 HOH HOH 2026 A HOH 2027 3 HOH HOH 2027 A HOH 2028 3 HOH HOH 2028 A HOH 2029 3 HOH HOH 2029 A HOH 2030 3 HOH HOH 2030 A HOH 2031 3 HOH HOH 2031 A HOH 2032 3 HOH HOH 2032 A HOH 2033 3 HOH HOH 2033 A HOH 2034 3 HOH HOH 2034 A HOH 2035 3 HOH HOH 2035 A HOH 2036 3 HOH HOH 2036 A HOH 2037 3 HOH HOH 2037 A HOH 2038 3 HOH HOH 2038 A HOH 2039 3 HOH HOH 2039 A HOH 2040 3 HOH HOH 2040 A HOH 2041 3 HOH HOH 2041 A HOH 2042 3 HOH HOH 2042 A HOH 2043 3 HOH HOH 2043 A HOH 2044 3 HOH HOH 2044 A HOH 2045 3 HOH HOH 2045 A HOH 2046 3 HOH HOH 2046 A HOH 2047 3 HOH HOH 2047 A HOH 2048 3 HOH HOH 2048 A HOH 2049 3 HOH HOH 2049 A HOH 2050 3 HOH HOH 2050 A HOH 2051 3 HOH HOH 2051 A HOH 2052 3 HOH HOH 2052 A HOH 2053 3 HOH HOH 2053 A HOH 2054 3 HOH HOH 2054 A HOH 2055 3 HOH HOH 2055 A HOH 2056 3 HOH HOH 2056 A HOH 2057 3 HOH HOH 2057 A HOH 2058 3 HOH HOH 2058 A HOH 2059 3 HOH HOH 2059 A HOH 2060 3 HOH HOH 2060 A HOH 2061 3 HOH HOH 2061 A HOH 2062 3 HOH HOH 2062 A HOH 2063 3 HOH HOH 2063 A HOH 2064 3 HOH HOH 2064 A HOH 2065 3 HOH HOH 2065 A HOH 2066 3 HOH HOH 2066 A HOH 2067 3 HOH HOH 2067 A HOH 2068 3 HOH HOH 2068 A HOH 2069 3 HOH HOH 2069 A HOH 2070 3 HOH HOH 2070 A HOH 2071 3 HOH HOH 2071 A HOH 2072 3 HOH HOH 2072 A HOH 2073 3 HOH HOH 2073 A HOH 2001 3 HOH HOH 2001 B HOH 2002 3 HOH HOH 2002 B HOH 2003 3 HOH HOH 2003 B HOH 2004 3 HOH HOH 2004 B HOH 2005 3 HOH HOH 2005 B HOH 2006 3 HOH HOH 2006 B HOH 2007 3 HOH HOH 2007 B HOH 2008 3 HOH HOH 2008 B HOH 2009 3 HOH HOH 2009 B HOH 2010 3 HOH HOH 2010 B HOH 2011 3 HOH HOH 2011 B HOH 2012 3 HOH HOH 2012 B HOH 2013 3 HOH HOH 2013 B HOH 2014 3 HOH HOH 2014 B HOH 2015 3 HOH HOH 2015 B HOH 2016 3 HOH HOH 2016 B HOH 2017 3 HOH HOH 2017 B HOH 2018 3 HOH HOH 2018 B HOH 2019 3 HOH HOH 2019 B HOH 2020 3 HOH HOH 2020 B HOH 2021 3 HOH HOH 2021 B HOH 2022 3 HOH HOH 2022 B HOH 2023 3 HOH HOH 2023 B HOH 2024 3 HOH HOH 2024 B HOH 2025 3 HOH HOH 2025 B HOH 2026 3 HOH HOH 2026 B HOH 2027 3 HOH HOH 2027 B HOH 2028 3 HOH HOH 2028 B HOH 2029 3 HOH HOH 2029 B HOH 2030 3 HOH HOH 2030 B HOH 2031 3 HOH HOH 2031 B HOH 2032 3 HOH HOH 2032 B HOH 2033 3 HOH HOH 2033 B HOH 2034 3 HOH HOH 2034 B HOH 2035 3 HOH HOH 2035 B HOH 2036 3 HOH HOH 2036 B HOH 2037 3 HOH HOH 2037 B HOH 2038 3 HOH HOH 2038 B HOH 2039 3 HOH HOH 2039 B HOH 2040 3 HOH HOH 2040 B HOH 2041 3 HOH HOH 2041 B HOH 2042 3 HOH HOH 2042 B HOH 2043 3 HOH HOH 2043 B HOH 2044 3 HOH HOH 2044 B HOH 2045 3 HOH HOH 2045 B HOH 2046 3 HOH HOH 2046 B HOH 2047 3 HOH HOH 2047 B HOH 2048 3 HOH HOH 2048 B HOH 2049 3 HOH HOH 2049 B HOH 2050 3 HOH HOH 2050 B HOH 2051 3 HOH HOH 2051 B HOH 2052 3 HOH HOH 2052 B HOH 2053 3 HOH HOH 2053 B HOH 2054 3 HOH HOH 2054 B HOH 2055 3 HOH HOH 2055 B HOH 2056 3 HOH HOH 2056 B HOH 2057 3 HOH HOH 2057 B HOH 2058 3 HOH HOH 2058 B HOH 2059 3 HOH HOH 2059 B HOH 2060 3 HOH HOH 2060 B HOH 2061 3 HOH HOH 2061 B HOH 2062 3 HOH HOH 2062 B HOH 2063 3 HOH HOH 2063 B DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A DC 3 n 3 DC 3 A DG 4 n 4 DG 4 A DA 5 n 5 DA 5 A DA 6 n 6 DA 6 A DT 7 n 7 DT 7 A DT 8 n 8 DT 8 A 5HC 9 n 9 5HC 9 A DG 10 n 10 DG 10 A DC 11 n 11 DC 11 A DG 12 n 12 DG 12 A DC 13 n 1 DC 13 B DG 14 n 2 DG 14 B DC 15 n 3 DC 15 B DG 16 n 4 DG 16 B DA 17 n 5 DA 17 B DA 18 n 6 DA 18 B DT 19 n 7 DT 19 B DT 20 n 8 DT 20 B 5HC 21 n 9 5HC 21 B DG 22 n 10 DG 22 B DC 23 n 11 DC 23 B DG 24 n 12 DG 24 B author_and_software_defined_assembly PISA 2 dimeric 1180 -6.7 4590 A HOH 2018 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2019 D O HOH 1_555 92.4 A HOH 2018 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2029 D O HOH 1_555 92.7 A HOH 2019 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2029 D O HOH 1_555 85.9 A HOH 2018 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2071 D O HOH 1_555 91.2 A HOH 2019 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2071 D O HOH 1_555 173.3 A HOH 2029 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2071 D O HOH 1_555 88.3 A HOH 2018 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2072 D O HOH 1_555 177.2 A HOH 2019 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2072 D O HOH 1_555 86.7 A HOH 2029 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2072 D O HOH 1_555 89.9 A HOH 2071 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2072 D O HOH 1_555 90.0 A HOH 2018 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2073 D O HOH 1_555 89.6 A HOH 2019 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2073 D O HOH 1_555 92.4 A HOH 2029 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2073 D O HOH 1_555 177.1 A HOH 2071 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2073 D O HOH 1_555 93.3 A HOH 2072 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 2073 D O HOH 1_555 87.8 A 5HC 9 A 5HC 9 DC B 5HC 21 B 5HC 9 DC 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A A O O HOH HOH 2009 2038 2.03 1 A A O O HOH HOH 2009 2034 2.15 1 A DC 11 0.060 SIDE CHAIN 1 B DC 23 0.095 SIDE CHAIN 1 -6.22 0.80 102.40 96.18 A A A C3' C2' C1' DG DG DG 4 4 4 N 1 -7.29 0.90 105.70 98.41 A A A O5' P OP2 DA DA DA 6 6 6 N 1 -10.69 0.90 105.70 95.01 A A A O5' P OP2 DG DG DG 10 10 10 N 1 -7.46 0.70 108.00 100.54 A A A O4' C1' N9 DG DG DG 12 12 12 N 1 -2.52 0.40 110.80 108.28 A A A C4 C5 N7 DG DG DG 12 12 12 N 1 3.06 0.40 105.40 108.46 A A A N9 C4 C5 DG DG DG 12 12 12 N 1 -6.43 0.70 108.00 101.57 B B B O4' C1' N1 DC DC DC 13 13 13 N 1 9.98 1.50 119.60 129.58 B B B OP1 P OP2 DG DG DG 14 14 14 N 1 -11.21 0.90 105.70 94.49 B B B O5' P OP2 DG DG DG 14 14 14 N 1 -11.34 1.60 120.90 109.56 B B B P O5' C5' DG DG DG 14 14 14 N 1 -8.10 1.00 110.10 102.00 B B B C1' O4' C4' DG DG DG 14 14 14 N 1 -5.65 0.70 108.00 102.35 B B B O4' C1' N9 DG DG DG 14 14 14 N 1 5.36 0.30 108.30 113.66 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 -3.41 0.50 129.30 125.89 B B B N1 C2 N3 DA DA DA 17 17 17 N 1 2.13 0.30 108.30 110.43 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 -3.37 0.40 104.50 101.13 B B B O4' C4' C3' DC DC DC 23 23 23 N 1 B B C2 O2 DC DC 13 13 -0.094 0.009 1.240 1.146 N 1 B B O3' C3' DG DG 14 14 -0.055 0.006 1.419 1.364 N 22.06 7.7695 0.0000 0.0000 -6.7934 0.0000 -0.9761 0.1734 0.1421 0.1452 1.3 34.2 2971 17362 10.15 93.78 0.14 1 0.0 MOLECULAR REPLACEMENT 16.50 0.29 0.50 PDB ENRTY 1BNA ML FLAT BULK SOLVENT MODEL 48.272 0.442 1.3 34.2 136 627 1 490 0 0.022 555 2.486 858 30.110 226 0.124 94 0.041 24 0.2261 0.1948 1.3213 130 1167 84.00 0.2134 0.1855 1.3441 121 1149 85.00 0.2285 0.1809 1.3685 136 1180 89.00 0.2393 0.1621 1.3949 137 1240 91.00 0.2242 0.1664 1.4233 135 1214 92.00 0.2022 0.1503 1.4543 142 1259 94.00 0.2397 0.1595 1.4881 147 1296 94.00 0.1885 0.1401 1.5253 139 1201 91.00 0.1947 0.1195 1.5666 141 1300 96.00 0.1627 0.1129 1.6127 146 1291 95.00 0.1261 0.1001 1.6647 144 1284 95.00 0.1537 0.0979 1.7242 142 1299 97.00 0.1331 0.1065 1.7932 149 1330 97.00 0.1795 0.1243 1.8749 146 1312 98.00 0.1921 0.1294 1.9737 147 1322 98.00 0.1572 0.1325 2.0973 141 1237 92.00 0.1952 0.1357 2.2592 148 1318 98.00 0.2007 0.1655 2.4865 146 1324 97.00 0.1917 0.1505 2.8462 149 1300 97.00 0.1664 0.1645 3.5853 141 1286 95.00 0.1432 0.1385 34.2269 144 1288 96.00 15.58 1.21 34.22 4C5X 19814 1.0 0.02 1 26.20 5.3 95.8 0.52 1.21 1.24 2.40 1 4.3 79.4 refinement PHENIX (PHENIX.REFINE) data reduction xia2 data scaling SCALA phasing PHASER Ultra High Resolution Dickerson-Drew dodecamer B-DNA with 5-Hydroxymethyl-cytosine Modification 1 N N 1 N N 2 N N 3 N N 3 N N covale 1.639 both A DT 8 A O3' DT 8 1_555 A 5HC 9 A P 5HC 9 1_555 covale 1.630 both A 5HC 9 A O3' 5HC 9 1_555 A DG 10 A P DG 10 1_555 covale 1.595 both B DT 20 B O3' DT 8 1_555 B 5HC 21 B P 5HC 9 1_555 covale 1.633 both B 5HC 21 B O3' 5HC 9 1_555 B DG 22 B P DG 10 1_555 metalc 2.055 A MG 101 C MG MG 1_555 A HOH 2018 D O HOH 1_555 metalc 2.066 A MG 101 C MG MG 1_555 A HOH 2019 D O HOH 1_555 metalc 2.038 A MG 101 C MG MG 1_555 A HOH 2029 D O HOH 1_555 metalc 2.098 A MG 101 C MG MG 1_555 A HOH 2071 D O HOH 1_555 metalc 2.102 A MG 101 C MG MG 1_555 A HOH 2072 D O HOH 1_555 metalc 2.113 A MG 101 C MG MG 1_555 A HOH 2073 D O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 24 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 24 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 24 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 23 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 23 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 23 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 22 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B 5HC 21 B N3 5HC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B 5HC 21 B O2 5HC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B 5HC 21 B N4 5HC 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 20 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 20 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 19 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 19 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 18 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 17 B N6 DA 5 1_555 hydrog WATSON-CRICK A 5HC 9 A N3 5HC 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A 5HC 9 A N4 5HC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A 5HC 9 A O2 5HC 9 1_555 B DG 16 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 15 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 14 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 14 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 14 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 1 1_555 DNA DNA, CYTOSINE MODIFICATION 4C5X PDB 1 4C5X 1 12 4C5X 1 12 4C5X A 1 1 12 13 24 4C5X 13 24 4C5X B 1 1 12 BINDING SITE FOR RESIDUE MG A 101 A MG 101 Software 6 A HOH 2018 D HOH 6 1_555 A HOH 2019 D HOH 6 1_555 A HOH 2029 D HOH 6 1_555 A HOH 2071 D HOH 6 1_555 A HOH 2072 D HOH 6 1_555 A HOH 2073 D HOH 6 1_555 19 P 21 21 21