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Crystal structure of a bright green fluorescent protein (StayGold) with double mutations (Q140S, Y187F) in jellyfish Cytaeis uchidae from Biortus
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 293 0.2 M Ammonium formate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.059 α = 90 b = 135.059 β = 90 c = 58.382 γ = 120
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 6M 2022-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 19.77 99.9 0.095 13.5 7.8 66929
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 1.174
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 AlphaFold 1.7 19.77 66901 3414 99.925 0.169 0.1677 0.179 0.198 0.2065 24.685
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] 0.573 0.286 0.573 -1.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.117 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_4_deg 11.805 r_dihedral_angle_1_deg 7.744 r_lrange_it 7.257 r_lrange_other 7.064 r_scangle_it 5.537 r_scangle_other 5.536 r_scbond_it 3.492 r_scbond_other 3.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.117 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_4_deg 11.805 r_dihedral_angle_1_deg 7.744 r_lrange_it 7.257 r_lrange_other 7.064 r_scangle_it 5.537 r_scangle_other 5.536 r_scbond_it 3.492 r_scbond_other 3.491 r_mcangle_other 3.28 r_mcangle_it 3.278 r_mcbond_it 2.282 r_mcbond_other 2.272 r_angle_refined_deg 1.818 r_angle_other_deg 1.428 r_nbd_other 0.205 r_symmetry_xyhbond_nbd_refined 0.205 r_nbd_refined 0.195 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.145 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_other 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3418 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing