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Crystal structure of beta-carotene-binding protein (BBP) from Schistocerca gregaria complexed with beta-carotene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.1 M Potassium acetate, pH 4.0, 0.2 M Potassium chloride, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.39 α = 90 b = 75.51 β = 90 c = 224.22 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 16M 2024-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.9792 SSRF BL17UM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.7 28.88 99.6 0.411 0.446 0.171 0.981 4.4 6.7 13341
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 99.6 2.85 3.089 1.178 0.31 6.8
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 2.7 28.88 12653 653 99.53 0.22412 0.22119 0.224 0.27766 0.2812 RANDOM 53.2
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] 0.39 -0.77 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.74 r_dihedral_angle_2_deg 17 r_long_range_B_refined 9.47 r_long_range_B_other 9.47 r_dihedral_angle_1_deg 8.34 r_scangle_other 6.897 r_mcangle_it 6.332 r_mcangle_other 6.332 r_scbond_it 4.452 r_scbond_other 4.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.74 r_dihedral_angle_2_deg 17 r_long_range_B_refined 9.47 r_long_range_B_other 9.47 r_dihedral_angle_1_deg 8.34 r_scangle_other 6.897 r_mcangle_it 6.332 r_mcangle_other 6.332 r_scbond_it 4.452 r_scbond_other 4.451 r_mcbond_it 4.172 r_mcbond_other 4.169 r_angle_refined_deg 2.313 r_angle_other_deg 1.062 r_chiral_restr 0.128 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_dihedral_angle_4_deg 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 3189 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing