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Crystal structure of a bright green fluorescent protein (StayGold) with double mutation (N137A, 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 Lithium sulfate,0.1 M BisTris pH5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.2 61.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.789 α = 90 b = 134.789 β = 90 c = 59.18 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 19.86 99.1 0.104 17.3 13.6 67008
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 0.968
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 19.86 66998 3428 99.129 0.154 0.1527 0.1646 0.1831 0.192 21.445
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] 0.454 0.227 0.454 -1.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.513 r_dihedral_angle_4_deg 13.12 r_dihedral_angle_3_deg 12.524 r_dihedral_angle_1_deg 7.3 r_lrange_it 7.226 r_lrange_other 7.035 r_scangle_it 5.666 r_scangle_other 5.665 r_scbond_it 3.634 r_scbond_other 3.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.513 r_dihedral_angle_4_deg 13.12 r_dihedral_angle_3_deg 12.524 r_dihedral_angle_1_deg 7.3 r_lrange_it 7.226 r_lrange_other 7.035 r_scangle_it 5.666 r_scangle_other 5.665 r_scbond_it 3.634 r_scbond_other 3.634 r_mcangle_other 2.564 r_mcangle_it 2.563 r_angle_refined_deg 1.85 r_mcbond_it 1.782 r_mcbond_other 1.779 r_angle_other_deg 1.429 r_symmetry_nbd_refined 0.299 r_symmetry_xyhbond_nbd_refined 0.266 r_nbd_other 0.235 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.17 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3406 Nucleic Acid Atoms Solvent Atoms 609 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing