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Bacterial chalcone isomerase H33A with taxifolin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 6.8 mg/ml CHI 50 mM Na phosphate, pH 6.8.
Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5.
Hanging drop 2+2 ul.
soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)
Crystal Properties Matthews coefficient Solvent content 4.95 75.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.582 α = 90 b = 203.736 β = 90 c = 560.388 γ = 90
Symmetry Space Group I 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.78 49.423 99.3 0.368 0.99 9.3 13.7 266311 42.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.78 2.95 98.2 1.58 0.24 1.76 13.3
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 THROUGHOUT 4D06 2.8 49.423 260531 2736 99.448 0.214 0.2134 0.217 0.2245 0.2274 66.89
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] 0.431 -0.232 -0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.628 r_dihedral_angle_3_deg 15.021 r_dihedral_angle_2_deg 9.205 r_dihedral_angle_1_deg 8.01 r_lrange_it 7.95 r_lrange_other 7.95 r_scangle_it 2.787 r_scangle_other 2.675 r_scbond_it 1.991 r_scbond_other 1.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.628 r_dihedral_angle_3_deg 15.021 r_dihedral_angle_2_deg 9.205 r_dihedral_angle_1_deg 8.01 r_lrange_it 7.95 r_lrange_other 7.95 r_scangle_it 2.787 r_scangle_other 2.675 r_scbond_it 1.991 r_scbond_other 1.876 r_mcangle_it 1.663 r_mcangle_other 1.663 r_angle_refined_deg 1.331 r_mcbond_it 0.966 r_mcbond_other 0.966 r_angle_other_deg 0.413 r_symmetry_nbd_refined 0.264 r_nbd_refined 0.209 r_nbd_other 0.204 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.136 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_151 0.059 r_chiral_restr 0.056 r_ncsr_local_group_142 0.055 r_ncsr_local_group_131 0.054 r_ncsr_local_group_153 0.054 r_ncsr_local_group_148 0.05 r_ncsr_local_group_82 0.049 r_ncsr_local_group_85 0.049 r_ncsr_local_group_132 0.049 r_ncsr_local_group_152 0.049 r_ncsr_local_group_61 0.048 r_ncsr_local_group_97 0.048 r_ncsr_local_group_125 0.048 r_ncsr_local_group_17 0.047 r_ncsr_local_group_116 0.047 r_ncsr_local_group_147 0.047 r_ncsr_local_group_32 0.046 r_ncsr_local_group_73 0.046 r_ncsr_local_group_124 0.046 r_ncsr_local_group_130 0.046 r_ncsr_local_group_150 0.046 r_ncsr_local_group_15 0.045 r_ncsr_local_group_117 0.045 r_ncsr_local_group_48 0.044 r_ncsr_local_group_75 0.044 r_ncsr_local_group_106 0.044 r_ncsr_local_group_115 0.044 r_ncsr_local_group_138 0.044 r_ncsr_local_group_143 0.044 r_ncsr_local_group_145 0.044 r_ncsr_local_group_146 0.044 r_ncsr_local_group_149 0.044 r_ncsr_local_group_47 0.043 r_ncsr_local_group_62 0.043 r_ncsr_local_group_86 0.043 r_ncsr_local_group_136 0.043 r_ncsr_local_group_137 0.043 r_ncsr_local_group_141 0.043 r_ncsr_local_group_46 0.042 r_ncsr_local_group_87 0.042 r_ncsr_local_group_107 0.042 r_ncsr_local_group_123 0.042 r_ncsr_local_group_12 0.041 r_ncsr_local_group_16 0.041 r_ncsr_local_group_70 0.041 r_ncsr_local_group_80 0.041 r_ncsr_local_group_96 0.041 r_ncsr_local_group_103 0.041 r_ncsr_local_group_128 0.041 r_ncsr_local_group_139 0.041 r_ncsr_local_group_31 0.04 r_ncsr_local_group_83 0.04 r_ncsr_local_group_108 0.04 r_ncsr_local_group_140 0.04 r_ncsr_local_group_5 0.039 r_ncsr_local_group_57 0.039 r_ncsr_local_group_84 0.039 r_ncsr_local_group_121 0.039 r_ncsr_local_group_21 0.038 r_ncsr_local_group_28 0.038 r_ncsr_local_group_33 0.038 r_ncsr_local_group_68 0.038 r_ncsr_local_group_74 0.038 r_ncsr_local_group_79 0.038 r_ncsr_local_group_104 0.038 r_ncsr_local_group_129 0.038 r_ncsr_local_group_20 0.037 r_ncsr_local_group_50 0.037 r_ncsr_local_group_58 0.037 r_ncsr_local_group_76 0.037 r_ncsr_local_group_78 0.037 r_ncsr_local_group_93 0.037 r_ncsr_local_group_98 0.037 r_ncsr_local_group_101 0.037 r_ncsr_local_group_118 0.037 r_ncsr_local_group_133 0.037 r_ncsr_local_group_10 0.036 r_ncsr_local_group_29 0.036 r_ncsr_local_group_43 0.036 r_ncsr_local_group_60 0.036 r_ncsr_local_group_67 0.036 r_ncsr_local_group_112 0.036 r_ncsr_local_group_26 0.035 r_ncsr_local_group_55 0.035 r_ncsr_local_group_64 0.035 r_ncsr_local_group_91 0.035 r_ncsr_local_group_126 0.035 r_ncsr_local_group_127 0.035 r_ncsr_local_group_49 0.034 r_ncsr_local_group_81 0.034 r_ncsr_local_group_120 0.034 r_ncsr_local_group_41 0.033 r_ncsr_local_group_94 0.033 r_ncsr_local_group_95 0.033 r_ncsr_local_group_23 0.032 r_ncsr_local_group_25 0.032 r_ncsr_local_group_36 0.032 r_ncsr_local_group_69 0.032 r_ncsr_local_group_110 0.032 r_ncsr_local_group_44 0.031 r_ncsr_local_group_71 0.031 r_ncsr_local_group_105 0.031 r_ncsr_local_group_113 0.031 r_ncsr_local_group_114 0.031 r_ncsr_local_group_4 0.03 r_ncsr_local_group_13 0.03 r_ncsr_local_group_30 0.03 r_ncsr_local_group_35 0.03 r_ncsr_local_group_52 0.03 r_ncsr_local_group_54 0.03 r_ncsr_local_group_59 0.03 r_ncsr_local_group_66 0.03 r_ncsr_local_group_72 0.03 r_ncsr_local_group_99 0.03 r_ncsr_local_group_109 0.03 r_ncsr_local_group_122 0.03 r_ncsr_local_group_134 0.03 r_ncsr_local_group_144 0.03 r_ncsr_local_group_53 0.029 r_ncsr_local_group_63 0.029 r_ncsr_local_group_65 0.029 r_ncsr_local_group_90 0.029 r_ncsr_local_group_100 0.029 r_ncsr_local_group_1 0.028 r_ncsr_local_group_3 0.028 r_ncsr_local_group_6 0.028 r_ncsr_local_group_77 0.028 r_ncsr_local_group_88 0.028 r_ncsr_local_group_9 0.027 r_ncsr_local_group_89 0.027 r_ncsr_local_group_7 0.026 r_ncsr_local_group_24 0.026 r_ncsr_local_group_45 0.026 r_ncsr_local_group_119 0.026 r_ncsr_local_group_8 0.025 r_ncsr_local_group_56 0.025 r_ncsr_local_group_102 0.025 r_ncsr_local_group_111 0.025 r_ncsr_local_group_11 0.024 r_ncsr_local_group_18 0.024 r_ncsr_local_group_40 0.024 r_ncsr_local_group_92 0.024 r_ncsr_local_group_135 0.024 r_ncsr_local_group_27 0.023 r_ncsr_local_group_38 0.023 r_ncsr_local_group_14 0.022 r_ncsr_local_group_34 0.022 r_ncsr_local_group_39 0.022 r_ncsr_local_group_37 0.021 r_ncsr_local_group_2 0.02 r_ncsr_local_group_19 0.019 r_ncsr_local_group_22 0.017 r_ncsr_local_group_51 0.017 r_ncsr_local_group_42 0.012 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 38176 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 875
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing