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Crystal structure of a bright green fluorescent protein (StayGold) with single mutation (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 sulfate,0.1 M BisTris pH5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.58 α = 90 b = 134.58 β = 90 c = 58.449 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 1.9 19.73 99.9 0.121 8.9 4.1 47721
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 1.9 1.94 0.626
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 1.9 19.73 47709 2364 99.82 0.162 0.1599 0.1703 0.2055 0.2111 20.252
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 0.229 0.459 -1.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.891 r_dihedral_angle_3_deg 12.619 r_dihedral_angle_4_deg 11.693 r_dihedral_angle_1_deg 7.647 r_lrange_it 6.07 r_lrange_other 5.736 r_scangle_it 3.608 r_scangle_other 3.584 r_scbond_it 2.217 r_scbond_other 2.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.891 r_dihedral_angle_3_deg 12.619 r_dihedral_angle_4_deg 11.693 r_dihedral_angle_1_deg 7.647 r_lrange_it 6.07 r_lrange_other 5.736 r_scangle_it 3.608 r_scangle_other 3.584 r_scbond_it 2.217 r_scbond_other 2.198 r_mcangle_it 2.154 r_mcangle_other 2.154 r_angle_refined_deg 1.567 r_mcbond_it 1.356 r_mcbond_other 1.354 r_angle_other_deg 1.283 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_refined 0.2 r_symmetry_nbd_other 0.181 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.129 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3424 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing