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Crystal structure of the unliganded microalgal AstaP-pink1 carotenoprotein
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, SITTING DROP 298 0.1M Tris pH 8.5, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.66 26.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.483 α = 90 b = 56.525 β = 90 c = 58.692 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 PILATUS 2M 2024-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.9772 LNLS SIRIUS MANACA
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 1.65 40.71 100 0.193 0.203 0.062 0.998 8.8 10.5 16831
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 1.65 1.68 100 3.096 3.256 0.996 0.416 10.4
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 1.65 40.71 15946 839 99.99 0.17827 0.17568 0.1875 0.22806 0.2379 RANDOM 26.331
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] -0.89 -0.12 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.803 r_dihedral_angle_2_deg 9.005 r_dihedral_angle_1_deg 8.638 r_long_range_B_refined 6.699 r_long_range_B_other 6.668 r_scangle_other 4.611 r_scbond_it 3.098 r_scbond_other 3.098 r_mcangle_it 2.995 r_mcangle_other 2.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.803 r_dihedral_angle_2_deg 9.005 r_dihedral_angle_1_deg 8.638 r_long_range_B_refined 6.699 r_long_range_B_other 6.668 r_scangle_other 4.611 r_scbond_it 3.098 r_scbond_other 3.098 r_mcangle_it 2.995 r_mcangle_other 2.995 r_angle_refined_deg 2.216 r_mcbond_it 1.976 r_mcbond_other 1.971 r_angle_other_deg 1.196 r_chiral_restr 0.179 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 1169 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing