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Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BUS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 30% PEG 4000, 0.2 M ammonium acetate, 0.1M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.61 α = 90 b = 97.47 β = 90 c = 157.54 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 2020-11-24 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) 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 1.83 50 100 0.22 0.997 12.94 15.66 75109
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 1.83 1.94 100 1.33 0.745 2.29 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.83 48.78 71283 3744 99.99 0.15194 0.1502 0.1626 0.18514 0.1953 RANDOM 22.515
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] -0.63 0.28 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.727 r_dihedral_angle_4_deg 17.665 r_dihedral_angle_3_deg 13.969 r_long_range_B_refined 6.974 r_long_range_B_other 6.838 r_dihedral_angle_1_deg 6.552 r_scangle_other 5.419 r_scbond_it 3.636 r_scbond_other 3.636 r_mcangle_other 2.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.727 r_dihedral_angle_4_deg 17.665 r_dihedral_angle_3_deg 13.969 r_long_range_B_refined 6.974 r_long_range_B_other 6.838 r_dihedral_angle_1_deg 6.552 r_scangle_other 5.419 r_scbond_it 3.636 r_scbond_other 3.636 r_mcangle_other 2.332 r_mcangle_it 2.327 r_angle_refined_deg 1.717 r_mcbond_it 1.71 r_mcbond_other 1.694 r_angle_other_deg 1.417 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5988 Nucleic Acid Atoms Solvent Atoms 703 Heterogen Atoms 207
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XDS data reduction XSCALE data scaling MOLREP phasing