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Crystal structure of a bright green fluorescent protein (StayGold) with triple mutations (N137A, Q140S, Y187F) 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 1 M Lithium chloride, 0.1 M Citrate pH4.0, 20% PEG6000
Crystal Properties Matthews coefficient Solvent content 1.85 33.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.88 α = 90 b = 86.938 β = 109.66 c = 72.741 γ = 90
Symmetry Space Group P 1 21 1
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 2022-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.18062 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 2.3 48.13 98.9 0.038 12.3 3 35613
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 2.3 2.38 0.153
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 AF2 predicted 2.3 43.507 35594 1806 98.817 0.2 0.1968 0.2003 0.253 0.2529 31.791
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] 2.286 0.04 -1.892 -0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.987 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_3_deg 15.311 r_dihedral_angle_1_deg 8.09 r_lrange_it 5.526 r_lrange_other 5.465 r_scangle_it 3.697 r_scangle_other 3.697 r_mcangle_it 3.298 r_mcangle_other 3.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.987 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_3_deg 15.311 r_dihedral_angle_1_deg 8.09 r_lrange_it 5.526 r_lrange_other 5.465 r_scangle_it 3.697 r_scangle_other 3.697 r_mcangle_it 3.298 r_mcangle_other 3.297 r_scbond_it 2.275 r_scbond_other 2.275 r_mcbond_it 2.049 r_mcbond_other 2.048 r_angle_refined_deg 1.59 r_angle_other_deg 1.173 r_symmetry_nbd_refined 0.225 r_nbd_other 0.195 r_symmetry_nbd_other 0.184 r_nbd_refined 0.182 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.049 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6692 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing