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Crystal structure of a bright green fluorescent protein (StayGold) with single mutation (Q140S) 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 NaCl, 0.1 M MES pH6.0, 20% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.78 55.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.154 α = 90 b = 135.154 β = 90 c = 58.508 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 1.75 19.78 99.9 0.101 20 14.8 61618
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 1.75 1.78 1.112
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 1.75 19.78 61591 3110 99.917 0.154 0.1523 0.1645 0.184 0.1932 23.273
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] 0.528 0.264 0.528 -1.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.648 r_dihedral_angle_3_deg 13.826 r_dihedral_angle_4_deg 12.722 r_dihedral_angle_1_deg 7.707 r_lrange_it 7.536 r_lrange_other 7.354 r_scangle_it 5.856 r_scangle_other 5.855 r_scbond_it 3.727 r_scbond_other 3.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.648 r_dihedral_angle_3_deg 13.826 r_dihedral_angle_4_deg 12.722 r_dihedral_angle_1_deg 7.707 r_lrange_it 7.536 r_lrange_other 7.354 r_scangle_it 5.856 r_scangle_other 5.855 r_scbond_it 3.727 r_scbond_other 3.726 r_mcangle_it 2.925 r_mcangle_other 2.925 r_mcbond_it 2.049 r_mcbond_other 2.048 r_angle_refined_deg 1.816 r_angle_other_deg 1.426 r_symmetry_nbd_refined 0.351 r_nbd_other 0.316 r_symmetry_xyhbond_nbd_refined 0.284 r_nbd_refined 0.207 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.17 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.064 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3420 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing