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Crystal structure of the first StART-like domain of Arabidopsis C2 and GRAM domain-containing (C2GR) protein in complex with beta-sitosterol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M imidazole & MES (pH 6.5), 12.5% MPD, and 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.894 α = 90 b = 73.894 β = 90 c = 142.607 γ = 120
Symmetry Space Group P 31 1 2
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 PILATUS3 R 200K-A 2022-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.79 50 94.8 0.1 0.999 18.4 6.9 10743
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 1.1 0.681
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 2.794 21.557 10739 561 94.859 0.224 0.2227 0.2248 0.2475 0.2486 75.627
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] -0.611 -0.305 -0.611 1.982
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.361 r_lrange_other 21.361 r_dihedral_angle_6_deg 16.192 r_scangle_it 14.271 r_scangle_other 14.267 r_mcangle_it 13.847 r_mcangle_other 13.843 r_dihedral_angle_3_deg 12.084 r_scbond_it 9.464 r_scbond_other 9.464
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.361 r_lrange_other 21.361 r_dihedral_angle_6_deg 16.192 r_scangle_it 14.271 r_scangle_other 14.267 r_mcangle_it 13.847 r_mcangle_other 13.843 r_dihedral_angle_3_deg 12.084 r_scbond_it 9.464 r_scbond_other 9.464 r_mcbond_it 9.402 r_mcbond_other 9.391 r_dihedral_angle_1_deg 7.596 r_dihedral_angle_2_deg 3.638 r_angle_refined_deg 1.652 r_angle_other_deg 0.577 r_symmetry_nbd_other 0.212 r_nbd_other 0.196 r_nbd_refined 0.187 r_nbtor_refined 0.183 r_symmetry_nbtor_other 0.087 r_symmetry_nbd_refined 0.081 r_chiral_restr 0.072 r_xyhbond_nbd_refined 0.064 r_symmetry_xyhbond_nbd_refined 0.031 r_ext_dist_refined_b 0.02 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2767 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing