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Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 30% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate (pH 5.6).
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.64 α = 90 b = 97.99 β = 90 c = 157.81 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 100 PIXEL DECTRIS EIGER X 9M 2019-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.00000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.82 47.73 100 0.181 0.188 0.999 15.76 13.35 1023907
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.93 99.9 1.868 1.946 0.705 1.78 12.72
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 6DXA 1.82 47.73 76721 3904 99.927 0.153 0.1506 0.1634 0.1926 0.2014 27.319
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] -1.821 0.561 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.283 r_dihedral_angle_4_deg 15.644 r_dihedral_angle_3_deg 13.881 r_lrange_it 7.786 r_lrange_other 7.705 r_dihedral_angle_1_deg 6.663 r_scangle_it 5.861 r_scangle_other 5.86 r_scbond_it 3.964 r_scbond_other 3.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.283 r_dihedral_angle_4_deg 15.644 r_dihedral_angle_3_deg 13.881 r_lrange_it 7.786 r_lrange_other 7.705 r_dihedral_angle_1_deg 6.663 r_scangle_it 5.861 r_scangle_other 5.86 r_scbond_it 3.964 r_scbond_other 3.954 r_mcangle_other 2.696 r_mcangle_it 2.691 r_mcbond_it 1.988 r_mcbond_other 1.975 r_angle_refined_deg 1.633 r_angle_other_deg 1.39 r_nbd_refined 0.207 r_nbd_other 0.191 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.129 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5978 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XSCALE data scaling MOLREP phasing