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Crystal Structure of Chalcone Syntase and Chalcone Isomerase-like Protein Complex from Physcomitrella patens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold CHS-CHIL complex model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, potassium citrate
Crystal Properties Matthews coefficient Solvent content 2.64 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.9 α = 74.438 b = 88.87 β = 74.318 c = 117.97 γ = 68.803
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 2023-10-19 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 1.92 50 98.9 0.17 0.986 5.16 2.89 216275
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 1.92 2.04 99.1 1.13 0.61 1.01 2.94
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.92 49.186 216275 10913 99.003 0.179 0.1773 0.1768 0.2126 0.2164 28.82
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] -0.798 -0.806 -0.882 -0.904 1.529 1.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.848 r_dihedral_angle_3_deg 14.28 r_lrange_it 6.702 r_lrange_other 6.62 r_scangle_it 6.269 r_scangle_other 6.269 r_dihedral_angle_1_deg 5.936 r_scbond_it 4.945 r_scbond_other 4.945 r_mcangle_it 4.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.848 r_dihedral_angle_3_deg 14.28 r_lrange_it 6.702 r_lrange_other 6.62 r_scangle_it 6.269 r_scangle_other 6.269 r_dihedral_angle_1_deg 5.936 r_scbond_it 4.945 r_scbond_other 4.945 r_mcangle_it 4.227 r_mcangle_other 4.226 r_dihedral_angle_2_deg 3.723 r_mcbond_it 3.634 r_mcbond_other 3.634 r_angle_refined_deg 1.538 r_angle_other_deg 0.709 r_symmetry_nbd_other 0.213 r_nbd_refined 0.208 r_nbd_other 0.182 r_chiral_restr 0.178 r_nbtor_refined 0.178 r_ncsr_local_group_12 0.131 r_ncsr_local_group_8 0.125 r_ncsr_local_group_10 0.125 r_ncsr_local_group_7 0.123 r_ncsr_local_group_6 0.117 r_ncsr_local_group_9 0.117 r_symmetry_nbd_refined 0.095 r_ncsr_local_group_11 0.094 r_ncsr_local_group_5 0.092 r_ncsr_local_group_3 0.091 r_ncsr_local_group_1 0.088 r_ncsr_local_group_2 0.088 r_ncsr_local_group_4 0.088 r_symmetry_nbtor_other 0.08 r_xyhbond_nbd_refined 0.077 r_symmetry_xyhbond_nbd_refined 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18156 Nucleic Acid Atoms Solvent Atoms 2644 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction XDS data scaling PHASER phasing