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Crystal structure of YhaJ effector binding domain (ligand-bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF_AFP67660F1 AF_AFP67660F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 2.8M sodium acetate trihydrate pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.18 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.745 α = 90 b = 215.745 β = 90 c = 264.158 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2022-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 35.01 95.5 0.082 0.996 10.1 3.6 107524
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 89.9 0.391 0.178 2.2 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AF_AFP67660F1 2.803 34.998 107523 5740 95.489 0.186 0.1838 0.1508 0.232 0.1878 66.276
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -45.61 -45.61 91.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.344 r_dihedral_angle_4_deg 25.028 r_dihedral_angle_3_deg 20.408 r_lrange_it 14.899 r_mcangle_it 11.394 r_scangle_it 10.867 r_scbond_it 8.106 r_mcbond_it 7.957 r_dihedral_angle_1_deg 6.713 r_angle_refined_deg 1.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.344 r_dihedral_angle_4_deg 25.028 r_dihedral_angle_3_deg 20.408 r_lrange_it 14.899 r_mcangle_it 11.394 r_scangle_it 10.867 r_scbond_it 8.106 r_mcbond_it 7.957 r_dihedral_angle_1_deg 6.713 r_angle_refined_deg 1.698 r_symmetry_nbd_refined 0.39 r_symmetry_xyhbond_nbd_refined 0.379 r_nbtor_refined 0.313 r_nbd_refined 0.259 r_metal_ion_refined 0.225 r_xyhbond_nbd_refined 0.214 r_ncsr_local_group_9 0.198 r_ncsr_local_group_13 0.193 r_ncsr_local_group_15 0.193 r_ncsr_local_group_3 0.191 r_ncsr_local_group_11 0.19 r_ncsr_local_group_104 0.19 r_ncsr_local_group_100 0.189 r_ncsr_local_group_7 0.188 r_ncsr_local_group_111 0.188 r_ncsr_local_group_78 0.187 r_ncsr_local_group_5 0.185 r_ncsr_local_group_59 0.185 r_ncsr_local_group_61 0.185 r_ncsr_local_group_80 0.185 r_ncsr_local_group_16 0.184 r_ncsr_local_group_102 0.184 r_ncsr_local_group_1 0.183 r_ncsr_local_group_32 0.183 r_ncsr_local_group_95 0.183 r_ncsr_local_group_108 0.183 r_ncsr_local_group_18 0.182 r_ncsr_local_group_42 0.182 r_ncsr_local_group_65 0.181 r_ncsr_local_group_84 0.181 r_ncsr_local_group_106 0.181 r_ncsr_local_group_38 0.18 r_ncsr_local_group_93 0.18 r_ncsr_local_group_113 0.18 r_ncsr_local_group_4 0.179 r_ncsr_local_group_20 0.179 r_ncsr_local_group_22 0.179 r_ncsr_local_group_82 0.179 r_ncsr_local_group_117 0.179 r_ncsr_local_group_40 0.178 r_ncsr_local_group_46 0.178 r_ncsr_local_group_49 0.178 r_ncsr_local_group_110 0.178 r_ncsr_local_group_23 0.177 r_ncsr_local_group_24 0.177 r_ncsr_local_group_28 0.177 r_ncsr_local_group_34 0.177 r_ncsr_local_group_36 0.177 r_ncsr_local_group_45 0.177 r_ncsr_local_group_63 0.177 r_ncsr_local_group_86 0.177 r_ncsr_local_group_99 0.177 r_ncsr_local_group_120 0.177 r_ncsr_local_group_12 0.176 r_ncsr_local_group_55 0.176 r_ncsr_local_group_68 0.176 r_ncsr_local_group_87 0.176 r_ncsr_local_group_92 0.176 r_ncsr_local_group_53 0.175 r_ncsr_local_group_57 0.175 r_ncsr_local_group_74 0.175 r_ncsr_local_group_115 0.175 r_ncsr_local_group_118 0.175 r_ncsr_local_group_2 0.174 r_ncsr_local_group_43 0.174 r_ncsr_local_group_51 0.174 r_ncsr_local_group_67 0.173 r_ncsr_local_group_72 0.173 r_ncsr_local_group_105 0.173 r_ncsr_local_group_6 0.172 r_ncsr_local_group_60 0.172 r_ncsr_local_group_70 0.172 r_ncsr_local_group_71 0.172 r_ncsr_local_group_76 0.172 r_ncsr_local_group_85 0.172 r_ncsr_local_group_89 0.172 r_ncsr_local_group_91 0.172 r_ncsr_local_group_112 0.172 r_ncsr_local_group_25 0.171 r_ncsr_local_group_26 0.171 r_ncsr_local_group_47 0.171 r_ncsr_local_group_50 0.171 r_ncsr_local_group_97 0.171 r_ncsr_local_group_8 0.17 r_ncsr_local_group_27 0.17 r_ncsr_local_group_30 0.17 r_ncsr_local_group_48 0.17 r_ncsr_local_group_88 0.17 r_ncsr_local_group_75 0.169 r_ncsr_local_group_103 0.169 r_ncsr_local_group_10 0.168 r_ncsr_local_group_119 0.168 r_ncsr_local_group_19 0.167 r_ncsr_local_group_66 0.167 r_ncsr_local_group_69 0.167 r_ncsr_local_group_101 0.167 r_ncsr_local_group_14 0.166 r_ncsr_local_group_44 0.166 r_ncsr_local_group_52 0.166 r_ncsr_local_group_90 0.166 r_ncsr_local_group_31 0.165 r_ncsr_local_group_114 0.165 r_ncsr_local_group_37 0.164 r_ncsr_local_group_39 0.164 r_ncsr_local_group_54 0.164 r_ncsr_local_group_56 0.163 r_ncsr_local_group_21 0.162 r_ncsr_local_group_29 0.162 r_ncsr_local_group_58 0.162 r_ncsr_local_group_17 0.161 r_ncsr_local_group_73 0.161 r_ncsr_local_group_94 0.161 r_ncsr_local_group_107 0.161 r_ncsr_local_group_62 0.159 r_ncsr_local_group_77 0.159 r_ncsr_local_group_41 0.158 r_ncsr_local_group_64 0.158 r_ncsr_local_group_96 0.158 r_ncsr_local_group_35 0.156 r_ncsr_local_group_79 0.155 r_ncsr_local_group_33 0.154 r_ncsr_local_group_81 0.154 r_ncsr_local_group_98 0.153 r_ncsr_local_group_116 0.151 r_ncsr_local_group_109 0.15 r_ncsr_local_group_83 0.145 r_chiral_restr 0.115 r_gen_planes_refined 0.011 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25300 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 466
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing