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Crystal structure of a bright green fluorescent protein (StayGold) with single mutation (K192Y) in jellyfish Cytaeis uchidae from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF2 predicted
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 2.75 55.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.707 α = 90 b = 134.707 β = 90 c = 58.568 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 EIGER X 9M 2022-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.946418 CLSI 08ID-1
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 2 44.235 98.8 0.261 7.9 9.3 40718
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 2 2.05 1.097 2.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AF2 predicted 2 44.235 40712 1969 98.811 0.194 0.1916 0.2361 0.2239 16.374
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] 0.459 0.23 0.459 -1.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 14.094 r_dihedral_angle_3_deg 13.095 r_dihedral_angle_1_deg 7.784 r_lrange_it 5.588 r_lrange_other 5.288 r_scangle_it 1.967 r_scangle_other 1.966 r_mcangle_it 1.716 r_mcangle_other 1.716
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 14.094 r_dihedral_angle_3_deg 13.095 r_dihedral_angle_1_deg 7.784 r_lrange_it 5.588 r_lrange_other 5.288 r_scangle_it 1.967 r_scangle_other 1.966 r_mcangle_it 1.716 r_mcangle_other 1.716 r_angle_refined_deg 1.529 r_angle_other_deg 1.22 r_scbond_it 1.177 r_scbond_other 1.176 r_mcbond_it 0.983 r_mcbond_other 0.983 r_nbd_refined 0.179 r_symmetry_nbd_other 0.179 r_xyhbond_nbd_refined 0.173 r_nbd_other 0.169 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.16 r_symmetry_nbd_refined 0.097 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3424 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing