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Chalcone synthase from Hordeum vulgare complexed with CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DXB 6DXB
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 3.16 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.805 α = 90 b = 98.963 β = 90 c = 138.11 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 2022-03-04 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 1.7 45.829 99.8 0.07 0.076 0.029 0.999 18.3 13.2 117451
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 1.7 1.73 1.334 1.44 0.536 0.885 13.7
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 6DXB 1.7 45.829 117356 5895 99.737 0.178 0.1766 0.1781 0.2046 0.2066 33.018
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] 1.958 0.672 -2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.489 r_dihedral_angle_4_deg 18.018 r_dihedral_angle_3_deg 12.851 r_lrange_it 7.169 r_lrange_other 7.154 r_scangle_it 6.483 r_scangle_other 6.483 r_dihedral_angle_1_deg 6.221 r_scbond_it 4.457 r_scbond_other 4.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.489 r_dihedral_angle_4_deg 18.018 r_dihedral_angle_3_deg 12.851 r_lrange_it 7.169 r_lrange_other 7.154 r_scangle_it 6.483 r_scangle_other 6.483 r_dihedral_angle_1_deg 6.221 r_scbond_it 4.457 r_scbond_other 4.457 r_mcangle_it 3.253 r_mcangle_other 3.252 r_mcbond_it 2.635 r_mcbond_other 2.633 r_angle_refined_deg 1.757 r_angle_other_deg 1.489 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.173 r_nbd_other 0.165 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.147 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5820 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing