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Chalcone synthase from Hordeum vulgare complexed with CoA and naringenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B32 8B32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1M MES/Imidazole pH6.5; 0.03M MgCl2 0.03M CaCl2; 16% Glycerol; 8% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.908 α = 90 b = 95.981 β = 90 c = 138.338 γ = 90
Symmetry Space Group P 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 291 PIXEL DECTRIS EIGER X 16M 2022-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 48.037 99.9 0.087 0.094 0.036 0.999 19.8 13.2 67109
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.465 0.503 0.19 0.979 13.5
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 8B32 2 48.037 67037 3335 99.869 0.161 0.1589 0.16 0.1934 0.1943 29.158
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] 0.315 2.247 -2.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 18.018 r_dihedral_angle_3_deg 13.995 r_lrange_it 7.175 r_lrange_other 7.152 r_scangle_it 6.271 r_scangle_other 6.27 r_dihedral_angle_1_deg 6.147 r_scbond_it 4.313 r_scbond_other 4.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 18.018 r_dihedral_angle_3_deg 13.995 r_lrange_it 7.175 r_lrange_other 7.152 r_scangle_it 6.271 r_scangle_other 6.27 r_dihedral_angle_1_deg 6.147 r_scbond_it 4.313 r_scbond_other 4.313 r_mcangle_it 3.326 r_mcangle_other 3.325 r_mcbond_it 2.546 r_mcbond_other 2.542 r_angle_refined_deg 1.658 r_angle_other_deg 1.445 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.187 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.144 r_nbd_other 0.139 r_chiral_restr 0.086 r_ncsr_local_group_1 0.082 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5804 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction DIMPLE model building PHASER phasing