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Chalcone synthase from Glycine max (L.) Merr (soybean)
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, SITTING DROP 5.6 293 30% PEG4000, 0.2M ammonium acetate and 0.1M sodium citrate (pH 5.6)
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.76 α = 90 b = 98.94 β = 90 c = 159.29 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 2.52 159.3 99.7 0.575 0.446 0.973 6.56 15.4 30056
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 2.52 2.67 99.9 4.306 4.459 0.201 1.08 13.88
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 2.52 49.519 30007 1492 99.784 0.193 0.1894 0.197 0.2536 0.2562 35.771
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] -5.072 3.745 1.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_dihedral_angle_3_deg 17.534 r_dihedral_angle_4_deg 14.944 r_dihedral_angle_1_deg 7.399 r_lrange_it 6.145 r_lrange_other 6.13 r_scangle_it 4.095 r_scangle_other 4.092 r_mcangle_other 3.266 r_mcangle_it 3.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_dihedral_angle_3_deg 17.534 r_dihedral_angle_4_deg 14.944 r_dihedral_angle_1_deg 7.399 r_lrange_it 6.145 r_lrange_other 6.13 r_scangle_it 4.095 r_scangle_other 4.092 r_mcangle_other 3.266 r_mcangle_it 3.265 r_scbond_it 2.426 r_scbond_other 2.419 r_mcbond_it 1.974 r_mcbond_other 1.971 r_angle_refined_deg 1.465 r_angle_other_deg 1.152 r_symmetry_xyhbond_nbd_refined 0.342 r_nbd_other 0.251 r_nbd_refined 0.199 r_symmetry_nbd_other 0.184 r_symmetry_nbd_refined 0.175 r_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.155 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.075 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5988 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XSCALE data scaling MOLREP phasing