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Chalcone synthase from Hordeum vulgare complexed with CoA and eriodictyol
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 277 0.1M MES/Imidazole pH6.5; 0.03M MgCl2 0.03M CaCl2; 16%Glycerol; 8% PEG4000
Crystal Properties Matthews coefficient Solvent content 3.15 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.884 α = 90 b = 97.817 β = 90 c = 137.928 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 2022-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 48.956 100 0.076 0.082 0.031 0.999 17 12.8 71897
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 2.04 0.985 1.071 0.419 0.947 12.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8B32 2 48.956 71816 3554 99.949 0.2 0.1984 0.2337 0.2461 47.623
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] 2.967 1.706 -4.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.946 r_dihedral_angle_4_deg 17.075 r_dihedral_angle_3_deg 14.952 r_lrange_other 8.475 r_lrange_it 8.468 r_scangle_it 7.068 r_scangle_other 7.067 r_dihedral_angle_1_deg 6.447 r_scbond_it 5.127 r_scbond_other 5.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.946 r_dihedral_angle_4_deg 17.075 r_dihedral_angle_3_deg 14.952 r_lrange_other 8.475 r_lrange_it 8.468 r_scangle_it 7.068 r_scangle_other 7.067 r_dihedral_angle_1_deg 6.447 r_scbond_it 5.127 r_scbond_other 5.126 r_mcangle_it 4.978 r_mcangle_other 4.978 r_mcbond_it 4.091 r_mcbond_other 4.091 r_angle_refined_deg 1.503 r_angle_other_deg 1.323 r_nbd_other 0.212 r_nbd_refined 0.198 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.154 r_xyhbond_nbd_refined 0.146 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.078 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5827 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing Coot model building